BIOL4800/6220_Fall2022_RTutorial
R Basic
Introduction
R as a calculator
1 + 100## [1] 1012^2## [1] 47/2## [1] 3.54-1## [1] 32*2## [1] 43+5*2## [1] 13(3+5)*2## [1] 162e2## [1] 2002/10000## [1] 2e-04sin(1)## [1] 0.841471log(1)## [1] 0exp(0)## [1] 11 == 1## [1] TRUE1 >= 1## [1] TRUE1 < 1## [1] FALSE1 != 2## [1] TRUEx <- 10
x## [1] 10x + x## [1] 20x - 5## [1] 5x^2## [1] 100y <- x+x
y## [1] 20Vectorization
1:5## [1] 1 2 3 4 52^(1:5)## [1] 2 4 8 16 32v <- 1:5
2^v## [1] 2 4 8 16 32log10(v)## [1] 0.0000000 0.3010300 0.4771213 0.6020600 0.6989700Environment
ls()## [1] "v" "x" "y"rm(v)ls()## [1] "x" "y"Package Management
installed.packages()## Package
## askpass "askpass"
## assertthat "assertthat"
## backports "backports"
## base64enc "base64enc"
## BayesFactor "BayesFactor"
## bayestestR "bayestestR"
## bit "bit"
## bit64 "bit64"
## blob "blob"
## brio "brio"
## broom "broom"
## bslib "bslib"
## BWStest "BWStest"
## cachem "cachem"
## callr "callr"
## cartogram "cartogram"
## cellranger "cellranger"
## classInt "classInt"
## cli "cli"
## clipr "clipr"
## coda "coda"
## colorspace "colorspace"
## contfrac "contfrac"
## correlation "correlation"
## covr "covr"
## cpp11 "cpp11"
## crayon "crayon"
## curl "curl"
## data.table "data.table"
## datawizard "datawizard"
## DBI "DBI"
## dbplyr "dbplyr"
## deldir "deldir"
## desc "desc"
## deSolve "deSolve"
## dichromat "dichromat"
## diffobj "diffobj"
## digest "digest"
## dplyr "dplyr"
## dtplyr "dtplyr"
## e1071 "e1071"
## effectsize "effectsize"
## ellipsis "ellipsis"
## elliptic "elliptic"
## evaluate "evaluate"
## extrafont "extrafont"
## extrafontdb "extrafontdb"
## fansi "fansi"
## farver "farver"
## fastmap "fastmap"
## forcats "forcats"
## fs "fs"
## gargle "gargle"
## gcookbook "gcookbook"
## gdtools "gdtools"
## generics "generics"
## ggplot2 "ggplot2"
## ggplot2movies "ggplot2movies"
## ggrepel "ggrepel"
## ggridges "ggridges"
## ggsignif "ggsignif"
## ggstatsplot "ggstatsplot"
## glue "glue"
## gmp "gmp"
## googledrive "googledrive"
## googlesheets4 "googlesheets4"
## gridExtra "gridExtra"
## gtable "gtable"
## haven "haven"
## hexbin "hexbin"
## highr "highr"
## hms "hms"
## hrbrthemes "hrbrthemes"
## htmltools "htmltools"
## httr "httr"
## hunspell "hunspell"
## hypergeo "hypergeo"
## ids "ids"
## insight "insight"
## installr "installr"
## interp "interp"
## isoband "isoband"
## jpeg "jpeg"
## jquerylib "jquerylib"
## jsonlite "jsonlite"
## knitr "knitr"
## kSamples "kSamples"
## labeling "labeling"
## latticeExtra "latticeExtra"
## lazyeval "lazyeval"
## lifecycle "lifecycle"
## lubridate "lubridate"
## magrittr "magrittr"
## mapproj "mapproj"
## maps "maps"
## maptools "maptools"
## markdown "markdown"
## Matrix "Matrix"
## MatrixModels "MatrixModels"
## mc2d "mc2d"
## memoise "memoise"
## mime "mime"
## modelr "modelr"
## multcompView "multcompView"
## munsell "munsell"
## mvtnorm "mvtnorm"
## openssl "openssl"
## packcircles "packcircles"
## paletteer "paletteer"
## palmerpenguins "palmerpenguins"
## parameters "parameters"
## patchwork "patchwork"
## pbapply "pbapply"
## performance "performance"
## permute "permute"
## pillar "pillar"
## pkgconfig "pkgconfig"
## pkgload "pkgload"
## plyr "plyr"
## PMCMRplus "PMCMRplus"
## png "png"
## praise "praise"
## prettyunits "prettyunits"
## prismatic "prismatic"
## processx "processx"
## progress "progress"
## proxy "proxy"
## ps "ps"
## purrr "purrr"
## R6 "R6"
## rappdirs "rappdirs"
## raster "raster"
## rasterVis "rasterVis"
## RColorBrewer "RColorBrewer"
## Rcpp "Rcpp"
## RcppEigen "RcppEigen"
## RcppParallel "RcppParallel"
## readr "readr"
## readxl "readxl"
## rematch "rematch"
## rematch2 "rematch2"
## reprex "reprex"
## reshape "reshape"
## rex "rex"
## rgdal "rgdal"
## rlang "rlang"
## rmarkdown "rmarkdown"
## Rmpfr "Rmpfr"
## rprojroot "rprojroot"
## rstantools "rstantools"
## rstudioapi "rstudioapi"
## Rttf2pt1 "Rttf2pt1"
## rvest "rvest"
## s2 "s2"
## sass "sass"
## scales "scales"
## selectr "selectr"
## sf "sf"
## sm "sm"
## sp "sp"
## statsExpressions "statsExpressions"
## stringi "stringi"
## stringr "stringr"
## SuppDists "SuppDists"
## svglite "svglite"
## sys "sys"
## systemfonts "systemfonts"
## terra "terra"
## testthat "testthat"
## tibble "tibble"
## tidyr "tidyr"
## tidyselect "tidyselect"
## tidyverse "tidyverse"
## tinytex "tinytex"
## tzdb "tzdb"
## units "units"
## utf8 "utf8"
## uuid "uuid"
## vctrs "vctrs"
## vdiffr "vdiffr"
## vegan "vegan"
## vioplot "vioplot"
## viridis "viridis"
## viridisLite "viridisLite"
## vroom "vroom"
## waldo "waldo"
## withr "withr"
## wk "wk"
## WRS2 "WRS2"
## xfun "xfun"
## xml2 "xml2"
## yaml "yaml"
## zeallot "zeallot"
## zoo "zoo"
## base "base"
## boot "boot"
## class "class"
## cluster "cluster"
## codetools "codetools"
## compiler "compiler"
## datasets "datasets"
## foreign "foreign"
## graphics "graphics"
## grDevices "grDevices"
## grid "grid"
## KernSmooth "KernSmooth"
## lattice "lattice"
## MASS "MASS"
## Matrix "Matrix"
## methods "methods"
## mgcv "mgcv"
## nlme "nlme"
## nnet "nnet"
## parallel "parallel"
## rpart "rpart"
## spatial "spatial"
## splines "splines"
## stats "stats"
## stats4 "stats4"
## survival "survival"
## tcltk "tcltk"
## tools "tools"
## translations "translations"
## utils "utils"
## LibPath Version
## askpass "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1"
## assertthat "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.2.1"
## backports "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.4.1"
## base64enc "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1-3"
## BayesFactor "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.9.12-4.4"
## bayestestR "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.13.0"
## bit "C:/Users/msbre/AppData/Local/R/win-library/4.2" "4.0.4"
## bit64 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "4.0.5"
## blob "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.3"
## brio "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.3"
## broom "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.1"
## bslib "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4.0"
## BWStest "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.2.2"
## cachem "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.6"
## callr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.7.2"
## cartogram "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.2.2"
## cellranger "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.0"
## classInt "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4-8"
## cli "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.4.1"
## clipr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8.0"
## coda "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.19-4"
## colorspace "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0-3"
## contfrac "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-12"
## correlation "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8.3"
## covr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.6.1"
## cpp11 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4.3"
## crayon "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5.2"
## curl "C:/Users/msbre/AppData/Local/R/win-library/4.2" "4.3.3"
## data.table "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.14.2"
## datawizard "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6.3"
## DBI "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.3"
## dbplyr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.2.1"
## deldir "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0-6"
## desc "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.4.2"
## deSolve "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.33"
## dichromat "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0-0.1"
## diffobj "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.5"
## digest "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6.29"
## dplyr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.10"
## dtplyr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.2"
## e1071 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.7-11"
## effectsize "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8.1"
## ellipsis "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.2"
## elliptic "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.4-0"
## evaluate "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.16"
## extrafont "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.18"
## extrafontdb "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0"
## fansi "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.3"
## farver "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.1.1"
## fastmap "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.0"
## forcats "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.5.2"
## fs "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5.2"
## gargle "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.1"
## gcookbook "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0"
## gdtools "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.2.4"
## generics "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1.3"
## ggplot2 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.3.6"
## ggplot2movies "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.0.1"
## ggrepel "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.9.1"
## ggridges "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.5.4"
## ggsignif "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6.4"
## ggstatsplot "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.9.5"
## glue "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.6.2"
## gmp "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6-6"
## googledrive "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.0"
## googlesheets4 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.1"
## gridExtra "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.3"
## gtable "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.1"
## haven "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.5.1"
## hexbin "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.28.2"
## highr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.9"
## hms "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.2"
## hrbrthemes "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8.0"
## htmltools "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.5.3"
## httr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.4.4"
## hunspell "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.0.2"
## hypergeo "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2-13"
## ids "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.1"
## insight "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.18.6"
## installr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.23.2"
## interp "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-3"
## isoband "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.2.5"
## jpeg "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1-9"
## jquerylib "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1.4"
## jsonlite "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.8.2"
## knitr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.40"
## kSamples "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2-9"
## labeling "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4.2"
## latticeExtra "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6-30"
## lazyeval "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.2.2"
## lifecycle "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.3"
## lubridate "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.8.0"
## magrittr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.3"
## mapproj "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.8"
## maps "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.4.0"
## maptools "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-4"
## markdown "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1"
## Matrix "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5-1"
## MatrixModels "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.5-1"
## mc2d "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1-21"
## memoise "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.1"
## mime "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.12"
## modelr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1.9"
## multcompView "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1-8"
## munsell "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.5.0"
## mvtnorm "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-3"
## openssl "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.3"
## packcircles "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.4"
## paletteer "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5.0"
## palmerpenguins "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1.1"
## parameters "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.19.0"
## patchwork "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.2"
## pbapply "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5-0"
## performance "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.10.0"
## permute "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.9-7"
## pillar "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.8.1"
## pkgconfig "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.3"
## pkgload "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.3.0"
## plyr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.8.7"
## PMCMRplus "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.9.6"
## png "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.1-7"
## praise "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.0"
## prettyunits "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.1"
## prismatic "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.1"
## processx "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.7.0"
## progress "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.2"
## proxy "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4-27"
## ps "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.7.1"
## purrr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.5"
## R6 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.5.1"
## rappdirs "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.3"
## raster "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.6-3"
## rasterVis "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.51.2"
## RColorBrewer "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-3"
## Rcpp "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.9"
## RcppEigen "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.3.9.2"
## RcppParallel "C:/Users/msbre/AppData/Local/R/win-library/4.2" "5.1.5"
## readr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.1.3"
## readxl "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.4.1"
## rematch "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.1"
## rematch2 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.1.2"
## reprex "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.2"
## reshape "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8.9"
## rex "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.1"
## rgdal "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5-32"
## rlang "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.6"
## rmarkdown "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.16"
## Rmpfr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8-9"
## rprojroot "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.0.3"
## rstantools "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.2.0"
## rstudioapi "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.14"
## Rttf2pt1 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.3.11"
## rvest "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.3"
## s2 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1.0"
## sass "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4.2"
## scales "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.1"
## selectr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4-2"
## sf "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0-8"
## sm "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.2-5.7.1"
## sp "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.5-0"
## statsExpressions "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.3.4"
## stringi "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.7.8"
## stringr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.4.1"
## SuppDists "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-9.7"
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## sys "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.4"
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## terra "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.6-17"
## testthat "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.1.5"
## tibble "C:/Users/msbre/AppData/Local/R/win-library/4.2" "3.1.8"
## tidyr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.1"
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## units "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.8-0"
## utf8 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.2.2"
## uuid "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-0"
## vctrs "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4.2"
## vdiffr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.0.4"
## vegan "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.6-2"
## vioplot "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.3.7"
## viridis "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6.2"
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## vroom "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.6.0"
## waldo "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.4.0"
## withr "C:/Users/msbre/AppData/Local/R/win-library/4.2" "2.5.0"
## wk "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.6.0"
## WRS2 "C:/Users/msbre/AppData/Local/R/win-library/4.2" "1.1-4"
## xfun "C:/Users/msbre/AppData/Local/R/win-library/4.2" "0.33"
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## compiler "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## datasets "C:/Program Files/R/R-4.2.1/library" "4.2.1"
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## parallel "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## rpart "C:/Program Files/R/R-4.2.1/library" "4.1.16"
## spatial "C:/Program Files/R/R-4.2.1/library" "7.3-15"
## splines "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## stats "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## stats4 "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## survival "C:/Program Files/R/R-4.2.1/library" "3.3-1"
## tcltk "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## tools "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## translations "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## utils "C:/Program Files/R/R-4.2.1/library" "4.2.1"
## Priority
## askpass NA
## assertthat NA
## backports NA
## base64enc NA
## BayesFactor NA
## bayestestR NA
## bit NA
## bit64 NA
## blob NA
## brio NA
## broom NA
## bslib NA
## BWStest NA
## cachem NA
## callr NA
## cartogram NA
## cellranger NA
## classInt NA
## cli NA
## clipr NA
## coda NA
## colorspace NA
## contfrac NA
## correlation NA
## covr NA
## cpp11 NA
## crayon NA
## curl NA
## data.table NA
## datawizard NA
## DBI NA
## dbplyr NA
## deldir NA
## desc NA
## deSolve NA
## dichromat NA
## diffobj NA
## digest NA
## dplyr NA
## dtplyr NA
## e1071 NA
## effectsize NA
## ellipsis NA
## elliptic NA
## evaluate NA
## extrafont NA
## extrafontdb NA
## fansi NA
## farver NA
## fastmap NA
## forcats NA
## fs NA
## gargle NA
## gcookbook NA
## gdtools NA
## generics NA
## ggplot2 NA
## ggplot2movies NA
## ggrepel NA
## ggridges NA
## ggsignif NA
## ggstatsplot NA
## glue NA
## gmp NA
## googledrive NA
## googlesheets4 NA
## gridExtra NA
## gtable NA
## haven NA
## hexbin NA
## highr NA
## hms NA
## hrbrthemes NA
## htmltools NA
## httr NA
## hunspell NA
## hypergeo NA
## ids NA
## insight NA
## installr NA
## interp NA
## isoband NA
## jpeg NA
## jquerylib NA
## jsonlite NA
## knitr NA
## kSamples NA
## labeling NA
## latticeExtra NA
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## lifecycle NA
## lubridate NA
## magrittr NA
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## MatrixModels NA
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## mime NA
## modelr NA
## multcompView NA
## munsell NA
## mvtnorm NA
## openssl NA
## packcircles NA
## paletteer NA
## palmerpenguins NA
## parameters NA
## patchwork NA
## pbapply NA
## performance NA
## permute NA
## pillar NA
## pkgconfig NA
## pkgload NA
## plyr NA
## PMCMRplus NA
## png NA
## praise NA
## prettyunits NA
## prismatic NA
## processx NA
## progress NA
## proxy NA
## ps NA
## purrr NA
## R6 NA
## rappdirs NA
## raster NA
## rasterVis NA
## RColorBrewer NA
## Rcpp NA
## RcppEigen NA
## RcppParallel NA
## readr NA
## readxl NA
## rematch NA
## rematch2 NA
## reprex NA
## reshape NA
## rex NA
## rgdal NA
## rlang NA
## rmarkdown NA
## Rmpfr NA
## rprojroot NA
## rstantools NA
## rstudioapi NA
## Rttf2pt1 NA
## rvest NA
## s2 NA
## sass NA
## scales NA
## selectr NA
## sf NA
## sm NA
## sp NA
## statsExpressions NA
## stringi NA
## stringr NA
## SuppDists NA
## svglite NA
## sys NA
## systemfonts NA
## terra NA
## testthat NA
## tibble NA
## tidyr NA
## tidyselect NA
## tidyverse NA
## tinytex NA
## tzdb NA
## units NA
## utf8 NA
## uuid NA
## vctrs NA
## vdiffr NA
## vegan NA
## vioplot NA
## viridis NA
## viridisLite NA
## vroom NA
## waldo NA
## withr NA
## wk NA
## WRS2 NA
## xfun NA
## xml2 NA
## yaml NA
## zeallot NA
## zoo NA
## base "base"
## boot "recommended"
## class "recommended"
## cluster "recommended"
## codetools "recommended"
## compiler "base"
## datasets "base"
## foreign "recommended"
## graphics "base"
## grDevices "base"
## grid "base"
## KernSmooth "recommended"
## lattice "recommended"
## MASS "recommended"
## Matrix "recommended"
## methods "base"
## mgcv "recommended"
## nlme "recommended"
## nnet "recommended"
## parallel "base"
## rpart "recommended"
## spatial "recommended"
## splines "base"
## stats "base"
## stats4 "base"
## survival "recommended"
## tcltk "base"
## tools "base"
## translations NA
## utils "base"
## Depends
## askpass NA
## assertthat NA
## backports "R (>= 3.0.0)"
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## bayestestR "R (>= 3.6)"
## bit "R (>= 2.9.2)"
## bit64 "R (>= 3.0.1), bit (>= 4.0.0), utils, methods, stats"
## blob NA
## brio NA
## broom "R (>= 3.1)"
## bslib "R (>= 2.10)"
## BWStest NA
## cachem NA
## callr "R (>= 3.4)"
## cartogram NA
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## classInt "R (>= 2.2)"
## cli "R (>= 3.4)"
## clipr NA
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## DBI "methods, R (>= 3.0.0)"
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## extrafontdb "R (>= 2.14)"
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## farver NA
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## gargle "R (>= 3.5)"
## gcookbook "R (>= 2.10)"
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## ggplot2 "R (>= 3.3)"
## ggplot2movies "R (>= 2.10.0)"
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## ggsignif NA
## ggstatsplot "R (>= 4.0.0)"
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## googledrive "R (>= 3.3)"
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## haven "R (>= 3.4)"
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## htmltools "R (>= 2.14.1)"
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## hypergeo "R (>= 3.1.0),"
## ids NA
## insight "R (>= 3.5)"
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## isoband NA
## jpeg "R (>= 2.9.0)"
## jquerylib NA
## jsonlite "methods"
## knitr "R (>= 3.3.0)"
## kSamples "SuppDists"
## labeling NA
## latticeExtra "R (>= 3.6.0), lattice"
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## mapproj "R (>= 3.0.0), maps (>= 2.3-0)"
## maps "R (>= 3.5.0)"
## maptools "R (>= 2.10), sp (>= 1.0-11)"
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## mc2d "R (>= 2.10.0), mvtnorm"
## memoise NA
## mime NA
## modelr "R (>= 3.2)"
## multcompView NA
## munsell NA
## mvtnorm "R(>= 3.5.0)"
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## pkgload "R (>= 3.4.0)"
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## progress NA
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## raster "sp (>= 1.4-5), R (>= 3.5.0)"
## rasterVis "R (>= 3.0.0), methods, lattice (>= 0.20-41)"
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## Rcpp NA
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## readxl "R (>= 3.4)"
## rematch NA
## rematch2 NA
## reprex "R (>= 3.4)"
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## rex NA
## rgdal "R (>= 3.5.0), methods, sp (>= 1.1-0)"
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## rmarkdown "R (>= 3.0)"
## Rmpfr "gmp (>= 0.6-1), R (>= 3.5.0)"
## rprojroot "R (>= 3.0.0)"
## rstantools NA
## rstudioapi NA
## Rttf2pt1 "R (>= 2.15)"
## rvest "R (>= 3.2)"
## s2 "R (>= 3.0.0)"
## sass NA
## scales "R (>= 3.2)"
## selectr "R (>= 3.0)"
## sf "methods, R (>= 3.3.0)"
## sm "R (>= 3.1.0)"
## sp "R (>= 3.0.0), methods"
## statsExpressions "R (>= 4.0.0)"
## stringi "R (>= 3.1)"
## stringr "R (>= 3.1)"
## SuppDists "R (>= 3.3.0)"
## svglite "R (>= 3.0.0)"
## sys NA
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## terra "R (>= 3.5.0)"
## testthat "R (>= 3.1)"
## tibble "R (>= 3.1.0)"
## tidyr "R (>= 3.1)"
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## tidyverse "R (>= 3.3)"
## tinytex NA
## tzdb "R (>= 3.4.0)"
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## utf8 "R (>= 2.10)"
## uuid "R (>= 2.9.0)"
## vctrs "R (>= 3.3)"
## vdiffr "R (>= 3.2.0)"
## vegan "permute (>= 0.9-0), lattice, R (>= 3.4.0)"
## vioplot "sm, zoo"
## viridis "R (>= 2.10), viridisLite (>= 0.4.0)"
## viridisLite "R (>= 2.10)"
## vroom "R (>= 3.4)"
## waldo NA
## withr "R (>= 3.2.0)"
## wk NA
## WRS2 "R (>= 3.2.0)"
## xfun NA
## xml2 "R (>= 3.1.0)"
## yaml NA
## zeallot NA
## zoo "R (>= 3.1.0), stats"
## base NA
## boot "R (>= 3.0.0), graphics, stats"
## class "R (>= 3.0.0), stats, utils"
## cluster "R (>= 3.5.0)"
## codetools "R (>= 2.1)"
## compiler NA
## datasets NA
## foreign "R (>= 4.0.0)"
## graphics NA
## grDevices NA
## grid NA
## KernSmooth "R (>= 2.5.0), stats"
## lattice "R (>= 3.0.0)"
## MASS "R (>= 3.3.0), grDevices, graphics, stats, utils"
## Matrix "R (>= 3.5.0)"
## methods NA
## mgcv "R (>= 3.6.0), nlme (>= 3.1-64)"
## nlme "R (>= 3.5.0)"
## nnet "R (>= 3.0.0), stats, utils"
## parallel NA
## rpart "R (>= 2.15.0), graphics, stats, grDevices"
## spatial "R (>= 3.0.0), graphics, stats, utils"
## splines NA
## stats NA
## stats4 NA
## survival "R (>= 3.5.0)"
## tcltk NA
## tools NA
## translations NA
## utils NA
## Imports
## askpass "sys (>= 2.1)"
## assertthat "tools"
## backports NA
## base64enc NA
## BayesFactor "pbapply, mvtnorm, stringr, utils, graphics, MatrixModels, Rcpp\n(>= 0.11.2), methods, hypergeo"
## bayestestR "insight (>= 0.18.2), datawizard (>= 0.5.1), graphics, methods,\nstats, utils"
## bit NA
## bit64 NA
## blob "methods, rlang, vctrs (>= 0.2.1)"
## brio NA
## broom "backports, dplyr (>= 1.0.0), ellipsis, generics (>= 0.0.2),\nglue, purrr, rlang, stringr, tibble (>= 3.0.0), tidyr (>=\n1.0.0), ggplot2"
## bslib "grDevices, htmltools (>= 0.5.2), jsonlite, sass (>= 0.4.0),\njquerylib (>= 0.1.3), rlang, cachem, memoise"
## BWStest "memoise, Rcpp (>= 0.12.3)"
## cachem "rlang, fastmap"
## callr "processx (>= 3.6.1), R6, utils"
## cartogram "methods, sf, packcircles"
## cellranger "rematch, tibble"
## classInt "grDevices, stats, graphics, e1071, class, KernSmooth"
## cli "utils"
## clipr "utils"
## coda "lattice"
## colorspace "graphics, grDevices, stats"
## contfrac NA
## correlation "bayestestR (>= 0.13.0), datasets, datawizard (>= 0.5.1),\ninsight (>= 0.18.4), parameters (>= 0.18.2), stats"
## covr "digest, stats, utils, jsonlite, rex, httr, crayon, withr (>=\n1.0.2), yaml"
## cpp11 NA
## crayon "grDevices, methods, utils"
## curl NA
## data.table "methods"
## datawizard "insight (>= 0.18.5), stats, utils"
## DBI NA
## dbplyr "assertthat (>= 0.2.0), blob (>= 1.2.0), cli (>= 3.3.0), DBI\n(>= 1.0.0), dplyr (>= 1.0.9), glue (>= 1.2.0), lifecycle (>=\n1.0.0), magrittr, methods, pillar (>= 1.5.0), purrr (>= 0.2.5),\nR6 (>= 2.2.2), rlang (>= 1.0.0), tibble (>= 1.4.2), tidyselect\n(>= 0.2.4), utils, vctrs (>= 0.4.1), withr"
## deldir "graphics, grDevices"
## desc "cli, R6, rprojroot, utils"
## deSolve "methods, graphics, grDevices, stats"
## dichromat NA
## diffobj "crayon (>= 1.3.2), tools, methods, utils, stats"
## digest "utils"
## dplyr "generics, glue (>= 1.3.2), lifecycle (>= 1.0.1), magrittr (>=\n1.5), methods, R6, rlang (>= 1.0.2), tibble (>= 2.1.3),\ntidyselect (>= 1.1.1), utils, vctrs (>= 0.4.1), pillar (>=\n1.5.1)"
## dtplyr "crayon, data.table (>= 1.13.0), dplyr (>= 1.0.3), ellipsis,\nglue, lifecycle, rlang, tibble, tidyselect, vctrs"
## e1071 "graphics, grDevices, class, stats, methods, utils, proxy"
## effectsize "bayestestR (>= 0.13.0), insight (>= 0.18.4), parameters (>=\n0.19.0), performance (>= 0.10.0), datawizard (>= 0.6.2), stats,\nutils"
## ellipsis "rlang (>= 0.3.0)"
## elliptic "MASS"
## evaluate "methods"
## extrafont "extrafontdb, grDevices, utils, Rttf2pt1"
## extrafontdb NA
## fansi "grDevices, utils"
## farver NA
## fastmap NA
## forcats "cli, ellipsis, glue, lifecycle, magrittr, rlang (>= 1.0.0),\ntibble, withr"
## fs "methods"
## gargle "cli (>= 3.0.0), fs (>= 1.3.1), glue (>= 1.3.0), httr (>=\n1.4.0), jsonlite, rappdirs, rlang (>= 1.0.0), rstudioapi,\nstats, utils, withr"
## gcookbook NA
## gdtools "Rcpp (>= 0.12.12), systemfonts (>= 0.1.1)"
## generics "methods"
## ggplot2 "digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband,\nMASS, mgcv, rlang (>= 0.4.10), scales (>= 0.5.0), stats,\ntibble, withr (>= 2.0.0)"
## ggplot2movies NA
## ggrepel "grid, Rcpp, rlang (>= 0.3.0), scales (>= 0.5.0)"
## ggridges "ggplot2 (>= 3.0.0), grid (>= 3.0.0), scales (>= 0.4.1), withr\n(>= 2.1.1)"
## ggsignif "ggplot2 (>= 3.3.5)"
## ggstatsplot "correlation (>= 0.8.3), datawizard (>= 0.6.2), dplyr, ggplot2,\nggrepel, ggsignif, glue, insight (>= 0.18.5), paletteer,\nparameters (>= 0.19.0), patchwork, performance (>= 0.10.0),\npurrr, rlang, stats, statsExpressions (>= 1.3.4), tidyr, utils"
## glue "methods"
## gmp "methods"
## googledrive "cli (>= 3.0.0), gargle (>= 1.2.0), glue (>= 1.4.2), httr,\njsonlite, lifecycle, magrittr, pillar, purrr (>= 0.2.3), rlang\n(>= 0.4.9), tibble (>= 2.0.0), utils, uuid, vctrs (>= 0.3.0),\nwithr"
## googlesheets4 "cellranger, cli (>= 3.0.0), curl, gargle (>= 1.2.0), glue (>=\n1.3.0), googledrive (>= 2.0.0), httr, ids, magrittr, methods,\npurrr, rematch2, rlang (>= 1.0.2), tibble (>= 2.1.1), utils,\nvctrs (>= 0.2.3)"
## gridExtra "gtable, grid, grDevices, graphics, utils"
## gtable "grid"
## haven "cli (>= 3.0.0), forcats (>= 0.2.0), hms, lifecycle, methods,\nreadr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect, vctrs\n(>= 0.3.0)"
## hexbin "lattice, grid, graphics, grDevices, stats, utils"
## highr "xfun (>= 0.18)"
## hms "ellipsis (>= 0.3.2), lifecycle, methods, pkgconfig, rlang,\nvctrs (>= 0.3.8)"
## hrbrthemes "ggplot2 (>= 3.3.0), grDevices, grid, scales, extrafont, knitr,\nrmarkdown, htmltools, tools, magrittr, gdtools"
## htmltools "utils, digest, grDevices, base64enc, rlang (>= 0.4.10),\nfastmap (>= 1.1.0)"
## httr "curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6"
## hunspell "Rcpp, digest"
## hypergeo "elliptic (>= 1.3-5), contfrac (>= 1.1-9), deSolve"
## ids "openssl, uuid"
## insight "methods, stats, utils"
## installr "stringr, utils"
## interp "Rcpp (>= 0.12.9), deldir"
## isoband "grid, utils"
## jpeg NA
## jquerylib "htmltools"
## jsonlite NA
## knitr "evaluate (>= 0.15), highr, methods, stringr (>= 0.6), yaml (>=\n2.1.19), xfun (>= 0.29), tools"
## kSamples "methods, graphics, stats"
## labeling "stats, graphics"
## latticeExtra "grid, stats, utils, grDevices, png, jpeg, RColorBrewer,\ninterp, MASS"
## lazyeval NA
## lifecycle "cli (>= 3.4.0), glue, rlang (>= 1.0.6)"
## lubridate "generics"
## magrittr NA
## mapproj "stats, graphics"
## maps "graphics, utils"
## maptools "foreign (>= 0.8), methods, grid, lattice, stats, utils,\ngrDevices"
## markdown "utils, xfun, mime (>= 0.3)"
## Matrix "methods, graphics, grid, stats, utils, lattice"
## MatrixModels "stats, methods, Matrix (>= 1.4-2)"
## mc2d "stats, grDevices, graphics, utils"
## memoise "rlang (>= 0.4.10), cachem"
## mime "tools"
## modelr "broom, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble,\ntidyr (>= 0.8.0), tidyselect, vctrs"
## multcompView "grid"
## munsell "colorspace, methods"
## mvtnorm "stats, methods"
## openssl "askpass"
## packcircles "Rcpp (>= 1.0.0)"
## paletteer "prismatic, rematch2, rlang, rstudioapi"
## palmerpenguins NA
## parameters "bayestestR (>= 0.12.1), datawizard (>= 0.6.0), insight (>=\n0.18.3), graphics, methods, stats, utils"
## patchwork "ggplot2 (>= 3.0.0), gtable, grid, stats, grDevices, utils,\ngraphics"
## pbapply "parallel"
## performance "bayestestR (>= 0.12.0), insight (>= 0.18.3), datawizard (>=\n0.5.1), methods, stats, utils"
## permute "stats"
## pillar "cli (>= 2.3.0), fansi, glue, lifecycle, rlang (>= 1.0.2), utf8\n(>= 1.1.0), utils, vctrs (>= 0.3.8)"
## pkgconfig "utils"
## pkgload "cli (>= 3.3.0), crayon, desc, fs, glue, methods, rlang (>=\n1.0.3), rprojroot, utils, withr (>= 2.4.3)"
## plyr "Rcpp (>= 0.11.0)"
## PMCMRplus "mvtnorm (>= 1.0), multcompView, gmp, Rmpfr, SuppDists,\nkSamples (>= 1.2.7), BWStest (>= 0.2.1), MASS, stats"
## png NA
## praise NA
## prettyunits NA
## prismatic "graphics, farver (>= 2.0.1), grDevices"
## processx "ps (>= 1.2.0), R6, utils"
## progress "hms, prettyunits, R6, crayon"
## proxy "stats, utils"
## ps "utils"
## purrr "magrittr (>= 1.5), rlang (>= 0.3.1)"
## R6 NA
## rappdirs NA
## raster "Rcpp, methods, terra (>= 1.6-16)"
## rasterVis "raster (>= 3.4-13), terra (>= 1.4-9), latticeExtra, stats,\nutils, parallel, grid, grDevices, RColorBrewer, hexbin, sp (>=\n1.0-6), zoo, viridisLite"
## RColorBrewer NA
## Rcpp "methods, utils"
## RcppEigen "Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils"
## RcppParallel NA
## readr "cli (>= 3.2.0), clipr, crayon, hms (>= 0.4.1), lifecycle (>=\n0.2.0), methods, R6, rlang, tibble, utils, vroom (>= 1.6.0)"
## readxl "cellranger, tibble (>= 2.0.1), utils"
## rematch NA
## rematch2 "tibble"
## reprex "callr (>= 3.6.0), cli (>= 3.2.0), clipr (>= 0.4.0), fs, glue,\nknitr (>= 1.23), lifecycle, rlang (>= 1.0.0), rmarkdown,\nrstudioapi, utils, withr (>= 2.3.0)"
## reshape "plyr"
## rex "lazyeval"
## rgdal "grDevices, graphics, stats, utils"
## rlang "utils"
## rmarkdown "bslib (>= 0.2.5.1), evaluate (>= 0.13), htmltools (>= 0.5.1),\njquerylib, jsonlite, knitr (>= 1.22), methods, stringr (>=\n1.2.0), tinytex (>= 0.31), tools, utils, xfun (>= 0.30), yaml\n(>= 2.1.19)"
## Rmpfr "stats, utils, methods"
## rprojroot NA
## rstantools "desc, stats, utils, Rcpp (>= 0.12.16), RcppParallel (>= 5.0.1)"
## rstudioapi NA
## Rttf2pt1 NA
## rvest "glue, cli, httr (>= 0.5), lifecycle (>= 1.0.0), magrittr,\nrlang (>= 1.0.0), selectr, tibble, xml2 (>= 1.3), withr"
## s2 "Rcpp, wk (>= 0.6.0)"
## sass "fs, rlang (>= 0.4.10), htmltools (>= 0.5.1), R6, rappdirs"
## scales "farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6,\nRColorBrewer, rlang (>= 1.0.0), viridisLite"
## selectr "methods, stringr, R6"
## sf "classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid,\nmagrittr, Rcpp (>= 0.12.18), s2 (>= 1.0.7), stats, tools, units\n(>= 0.7-0), utils"
## sm NA
## sp "utils, stats, graphics, grDevices, lattice, grid"
## statsExpressions "BayesFactor (>= 0.9.12-4.4), correlation (>= 0.8.3),\ndatawizard (>= 0.6.2), dplyr, effectsize (>= 0.8.0), glue,\ninsight (>= 0.18.4), magrittr, parameters (>= 0.19.0),\nperformance (>= 0.10.0), rlang, stats, tibble, tidyr, WRS2 (>=\n1.1-4), zeallot"
## stringi "tools, utils, stats"
## stringr "glue (>= 1.2.0), magrittr, stringi (>= 1.1.7)"
## SuppDists NA
## svglite "systemfonts (>= 1.0.0)"
## sys NA
## systemfonts NA
## terra "methods, Rcpp"
## testthat "brio, callr (>= 3.5.1), cli (>= 3.4.0), desc, digest, ellipsis\n(>= 0.2.0), evaluate, jsonlite, lifecycle, magrittr, methods,\npkgload, praise, processx, ps (>= 1.3.4), R6 (>= 2.2.0), rlang\n(>= 1.0.1), utils, waldo (>= 0.4.0), withr (>= 2.4.3)"
## tibble "fansi (>= 0.4.0), lifecycle (>= 1.0.0), magrittr, methods,\npillar (>= 1.7.0), pkgconfig, rlang (>= 1.0.2), utils, vctrs\n(>= 0.3.8)"
## tidyr "dplyr (>= 1.0.0), ellipsis (>= 0.1.0), glue, lifecycle,\nmagrittr, purrr, rlang, tibble (>= 2.1.1), tidyselect (>=\n1.1.0), utils, vctrs (>= 0.3.7)"
## tidyselect "cli (>= 3.3.0), glue (>= 1.3.0), lifecycle (>= 1.0.3), rlang\n(>= 1.0.4), vctrs (>= 0.4.1), withr"
## tidyverse "broom (>= 0.7.10), cli (>= 3.1.0), crayon (>= 1.4.2), dbplyr\n(>= 2.1.1), dplyr (>= 1.0.7), dtplyr (>= 1.2.0), forcats (>=\n0.5.1), ggplot2 (>= 3.3.5), googledrive (>= 2.0.0),\ngooglesheets4 (>= 1.0.0), haven (>= 2.4.3), hms (>= 1.1.1),\nhttr (>= 1.4.2), jsonlite (>= 1.7.2), lubridate (>= 1.8.0),\nmagrittr (>= 2.0.1), modelr (>= 0.1.8), pillar (>= 1.6.4),\npurrr (>= 0.3.4), readr (>= 2.1.1), readxl (>= 1.3.1), reprex\n(>= 2.0.1), rlang (>= 0.4.12), rstudioapi (>= 0.13), rvest (>=\n1.0.2), stringr (>= 1.4.0), tibble (>= 3.1.6), tidyr (>=\n1.1.4), xml2 (>= 1.3.3)"
## tinytex "xfun (>= 0.29)"
## tzdb NA
## units "Rcpp"
## utf8 NA
## uuid NA
## vctrs "cli (>= 3.2.0), glue, rlang (>= 1.0.2)"
## vdiffr "diffobj, glue, grDevices, htmltools, lifecycle, rlang,\ntestthat (>= 3.0.3), xml2 (>= 1.0.0)"
## vegan "MASS, cluster, mgcv"
## vioplot NA
## viridis "stats, ggplot2 (>= 1.0.1), gridExtra"
## viridisLite NA
## vroom "bit64, cli (>= 3.2.0), crayon, glue, hms, lifecycle, methods,\nrlang (>= 0.4.2), stats, tibble (>= 2.0.0), tidyselect, tzdb\n(>= 0.1.1), vctrs (>= 0.2.0), withr"
## waldo "cli, diffobj (>= 0.3.4), fansi, glue, methods, rematch2, rlang\n(>= 1.0.0), tibble"
## withr "graphics, grDevices, stats"
## wk NA
## WRS2 "MASS, reshape, plyr, stats, graphics, grDevices, utils, mc2d"
## xfun "stats, tools"
## xml2 "methods"
## yaml NA
## zeallot NA
## zoo "utils, graphics, grDevices, lattice (>= 0.20-27)"
## base NA
## boot NA
## class "MASS"
## cluster "graphics, grDevices, stats, utils"
## codetools NA
## compiler NA
## datasets NA
## foreign "methods, utils, stats"
## graphics "grDevices"
## grDevices NA
## grid "grDevices, utils"
## KernSmooth NA
## lattice "grid, grDevices, graphics, stats, utils"
## MASS "methods"
## Matrix "methods, graphics, grid, stats, utils, lattice"
## methods "utils, stats"
## mgcv "methods, stats, graphics, Matrix, splines, utils"
## nlme "graphics, stats, utils, lattice"
## nnet NA
## parallel "tools, compiler"
## rpart NA
## spatial NA
## splines "graphics, stats"
## stats "utils, grDevices, graphics"
## stats4 "graphics, methods, stats"
## survival "graphics, Matrix, methods, splines, stats, utils"
## tcltk "utils"
## tools NA
## translations NA
## utils NA
## LinkingTo
## askpass NA
## assertthat NA
## backports NA
## base64enc NA
## BayesFactor "Rcpp (>= 0.11.2), RcppEigen (>= 0.3.2.2.0)"
## bayestestR NA
## bit NA
## bit64 NA
## blob NA
## brio NA
## broom NA
## bslib NA
## BWStest "Rcpp"
## cachem NA
## callr NA
## cartogram NA
## cellranger NA
## classInt NA
## cli NA
## clipr NA
## coda NA
## colorspace NA
## contfrac NA
## correlation NA
## covr NA
## cpp11 NA
## crayon NA
## curl NA
## data.table NA
## datawizard NA
## DBI NA
## dbplyr NA
## deldir NA
## desc NA
## deSolve NA
## dichromat NA
## diffobj NA
## digest NA
## dplyr NA
## dtplyr NA
## e1071 NA
## effectsize NA
## ellipsis NA
## elliptic NA
## evaluate NA
## extrafont NA
## extrafontdb NA
## fansi NA
## farver NA
## fastmap NA
## forcats NA
## fs NA
## gargle NA
## gcookbook NA
## gdtools "Rcpp"
## generics NA
## ggplot2 NA
## ggplot2movies NA
## ggrepel "Rcpp"
## ggridges NA
## ggsignif NA
## ggstatsplot NA
## glue NA
## gmp NA
## googledrive NA
## googlesheets4 NA
## gridExtra NA
## gtable NA
## haven "cpp11"
## hexbin NA
## highr NA
## hms NA
## hrbrthemes NA
## htmltools NA
## httr NA
## hunspell "Rcpp (>= 0.12.12)"
## hypergeo NA
## ids NA
## insight NA
## installr NA
## interp "Rcpp, RcppEigen"
## isoband NA
## jpeg NA
## jquerylib NA
## jsonlite NA
## knitr NA
## kSamples NA
## labeling NA
## latticeExtra NA
## lazyeval NA
## lifecycle NA
## lubridate "cpp11 (>= 0.2.7)"
## magrittr NA
## mapproj NA
## maps NA
## maptools NA
## markdown NA
## Matrix NA
## MatrixModels NA
## mc2d NA
## memoise NA
## mime NA
## modelr NA
## multcompView NA
## munsell NA
## mvtnorm NA
## openssl NA
## packcircles "Rcpp (>= 1.0.0)"
## paletteer NA
## palmerpenguins NA
## parameters NA
## patchwork NA
## pbapply NA
## performance NA
## permute NA
## pillar NA
## pkgconfig NA
## pkgload NA
## plyr "Rcpp"
## PMCMRplus NA
## png NA
## praise NA
## prettyunits NA
## prismatic NA
## processx NA
## progress NA
## proxy NA
## ps NA
## purrr NA
## R6 NA
## rappdirs NA
## raster "Rcpp"
## rasterVis NA
## RColorBrewer NA
## Rcpp NA
## RcppEigen "Rcpp"
## RcppParallel NA
## readr "cpp11, tzdb (>= 0.1.1)"
## readxl "cpp11 (>= 0.4.0), progress"
## rematch NA
## rematch2 NA
## reprex NA
## reshape NA
## rex NA
## rgdal "sp"
## rlang NA
## rmarkdown NA
## Rmpfr NA
## rprojroot NA
## rstantools NA
## rstudioapi NA
## Rttf2pt1 NA
## rvest NA
## s2 "Rcpp, wk"
## sass NA
## scales NA
## selectr NA
## sf "Rcpp"
## sm NA
## sp NA
## statsExpressions NA
## stringi NA
## stringr NA
## SuppDists NA
## svglite "cpp11, systemfonts"
## sys NA
## systemfonts "cpp11 (>= 0.2.1)"
## terra "Rcpp"
## testthat NA
## tibble NA
## tidyr "cpp11 (>= 0.4.0)"
## tidyselect NA
## tidyverse NA
## tinytex NA
## tzdb "cpp11 (>= 0.4.2)"
## units "Rcpp (>= 0.12.10)"
## utf8 NA
## uuid NA
## vctrs NA
## vdiffr "cpp11"
## vegan NA
## vioplot NA
## viridis NA
## viridisLite NA
## vroom "cpp11 (>= 0.2.0), progress (>= 1.2.1), tzdb (>= 0.1.1)"
## waldo NA
## withr NA
## wk NA
## WRS2 NA
## xfun NA
## xml2 NA
## yaml NA
## zeallot NA
## zoo NA
## base NA
## boot NA
## class NA
## cluster NA
## codetools NA
## compiler NA
## datasets NA
## foreign NA
## graphics NA
## grDevices NA
## grid NA
## KernSmooth NA
## lattice NA
## MASS NA
## Matrix NA
## methods NA
## mgcv NA
## nlme NA
## nnet NA
## parallel NA
## rpart NA
## spatial NA
## splines NA
## stats NA
## stats4 NA
## survival NA
## tcltk NA
## tools NA
## translations NA
## utils NA
## Suggests
## askpass "testthat"
## assertthat "testthat, covr"
## backports NA
## base64enc NA
## BayesFactor "doMC, foreach, testthat, knitr, markdown, arm, lme4, xtable,\nlanguageR"
## bayestestR "BayesFactor, bayesQR, bayesplot, BH, blavaan, bridgesampling,\nbrms, effectsize, emmeans, gamm4, ggdist, ggplot2, glmmTMB,\nhttr, KernSmooth, knitr, lavaan, lme4, logspline, MASS, mclust,\nmediation, modelbased, parameters, patchwork, performance,\nquadprog, posterior, RcppEigen, rmarkdown, rstan, rstanarm,\nsee, testthat, tweedie"
## bit "testthat (>= 0.11.0), roxygen2, knitr, rmarkdown,\nmicrobenchmark, bit64 (>= 4.0.0), ff (>= 4.0.0)"
## bit64 NA
## blob "covr, crayon, pillar (>= 1.2.1), testthat"
## brio "covr, testthat (>= 2.1.0)"
## broom "AER, AUC, bbmle, betareg, biglm, binGroup, boot, btergm (>=\n1.10.6), car, carData, caret, cluster, cmprsk, coda, covr, drc,\ne1071, emmeans, epiR, ergm (>= 3.10.4), fixest (>= 0.9.0), gam\n(>= 1.15), gee, geepack, glmnet, glmnetUtils, gmm, Hmisc,\nirlba, interp, joineRML, Kendall, knitr, ks, Lahman, lavaan,\nleaps, lfe, lm.beta, lme4, lmodel2, lmtest (>= 0.9.38),\nlsmeans, maps, maptools, margins, MASS, mclust, mediation,\nmetafor, mfx, mgcv, mlogit, modeldata, modeltests, muhaz,\nmultcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, poLCA,\npsych, quantreg, rgeos, rmarkdown, robust, robustbase, rsample,\nsandwich, sp, spdep (>= 1.1), spatialreg, speedglm, spelling,\nsurvey, survival, systemfit, testthat (>= 2.1.0), tseries,\nvars, zoo"
## bslib "shiny (>= 1.6.0), rmarkdown (>= 2.7), thematic, knitr,\ntestthat, withr, rappdirs, curl, magrittr"
## BWStest "testthat"
## cachem "testthat"
## callr "cli (>= 1.1.0), covr, mockery, ps, rprojroot, spelling,\ntestthat (>= 3.0.0), withr (>= 2.3.0)"
## cartogram "rgeos, sp, rgdal, maptools"
## cellranger "covr, testthat (>= 1.0.0), knitr, rmarkdown"
## classInt "spData (>= 0.2.6.2), units, knitr, rmarkdown"
## cli "callr, covr, digest, glue (>= 1.6.0), grDevices, htmltools,\nhtmlwidgets, knitr, methods, mockery, processx, ps (>=\n1.3.4.9000), rlang (>= 1.0.2.9003), rmarkdown, rprojroot,\nrstudioapi, testthat, tibble, whoami, withr"
## clipr "covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>=\n2.0.0)"
## coda NA
## colorspace "datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd,\ntcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg,\nknitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis,\nwesanderson"
## contfrac NA
## correlation "BayesFactor, poorman, energy, ggplot2, ggraph, gt, Hmisc,\nknitr, lme4, mbend, polycor, ppcor, psych, rmarkdown, rmcorr,\nrstanarm, see, testthat (>= 3.1.0), tidygraph, wdm, WRS2"
## covr "R6, curl, knitr, rmarkdown, htmltools, DT (>= 0.2), testthat,\nrlang, rstudioapi (>= 0.2), xml2 (>= 1.0.0), parallel, memoise,\nmockery, covr"
## cpp11 "bench, brio, callr, cli, covr, decor, desc, ggplot2, glue,\nknitr, lobstr, mockery, progress, rmarkdown, scales, Rcpp,\ntestthat, tibble, utils, vctrs, withr"
## crayon "mockery, rstudioapi, testthat, withr"
## curl "spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown,\nmagrittr, httpuv (>= 1.4.4), webutils"
## data.table "bit64 (>= 4.0.0), bit (>= 4.0.4), curl, R.utils, xts,\nnanotime, zoo (>= 1.8-1), yaml, knitr, rmarkdown"
## datawizard "bayestestR, boot, brms, data.table, dplyr (>= 1.0),\neffectsize, gamm4, ggplot2, haven, htmltools, httr, knitr,\nlme4, mediation, parameters, poorman (>= 0.2.6), psych, readxl,\nreadr, rio, rmarkdown, rstanarm, see, testthat (>= 3.1.0),\ntidyr, withr"
## DBI "blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms,\nknitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>=\n1.1-2), testthat, xml2"
## dbplyr "bit64, covr, knitr, Lahman, nycflights13, odbc, RMariaDB (>=\n1.0.2), rmarkdown, RPostgres (>= 1.1.3), RPostgreSQL, RSQLite\n(>= 2.1.0), testthat (>= 3.0.2), tidyr (>= 1.2.0)"
## deldir "polyclip"
## desc "callr, covr, gh, spelling, testthat, whoami, withr"
## deSolve "scatterplot3d, FME"
## dichromat NA
## diffobj "knitr, rmarkdown"
## digest "tinytest, simplermarkdown"
## dplyr "bench, broom, callr, covr, DBI, dbplyr (>= 1.4.3), ggplot2,\nknitr, Lahman, lobstr, microbenchmark, nycflights13, purrr,\nrmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat (>= 3.1.1),\ntidyr, withr"
## dtplyr "bench, covr, knitr, rmarkdown, testthat (>= 3.0.0), tidyr (>=\n1.1.0)"
## e1071 "cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable,\nMatrix, MASS, slam"
## effectsize "correlation (>= 0.8.2), see (>= 0.7.3), afex, BayesFactor,\nboot, brms, car, emmeans, knitr, lavaan, lme4, lmerTest, MASS,\nmgcv, parsnip, rmarkdown, rms, rstanarm, rstantools, testthat\n(>= 3.1.0)"
## ellipsis "covr, testthat"
## elliptic "emulator, calibrator (>= 1.2-8)"
## evaluate "covr, ggplot2, lattice, testthat"
## extrafont "fontcm"
## extrafontdb NA
## fansi "unitizer, knitr, rmarkdown"
## farver "covr, testthat (>= 3.0.0)"
## fastmap "testthat (>= 2.1.1)"
## forcats "covr, dplyr, ggplot2, knitr, readr, rmarkdown, testthat (>=\n3.0.0)"
## fs "testthat, covr, pillar (>= 1.0.0), tibble (>= 1.1.0), crayon,\nrmarkdown, knitr, withr, spelling, vctrs (>= 0.3.0)"
## gargle "aws.ec2metadata, aws.signature, covr, httpuv, knitr, mockr,\nrmarkdown, sodium, spelling, testthat (>= 3.1.2)"
## gcookbook NA
## gdtools "htmltools, testthat, fontquiver (>= 0.2.0), curl"
## generics "covr, pkgload, testthat (>= 3.0.0), tibble, withr"
## ggplot2 "covr, ragg, dplyr, ggplot2movies, hexbin, Hmisc, interp,\nknitr, lattice, mapproj, maps, maptools, multcomp, munsell,\nnlme, profvis, quantreg, RColorBrewer, rgeos, rmarkdown, rpart,\nsf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0),\nvdiffr (>= 1.0.0), xml2"
## ggplot2movies NA
## ggrepel "knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc,\nggbeeswarm, dplyr, magrittr, readr, stringr"
## ggridges "covr, dplyr, patchwork, ggplot2movies, forcats, knitr,\nrmarkdown, testthat, vdiffr"
## ggsignif "knitr, rmarkdown, testthat, vdiffr (>= 1.0.2)"
## ggstatsplot "afex, BayesFactor (>= 0.9.12-4.4), gapminder, ggcorrplot,\nggside, knitr, lme4, MASS, metaBMA, metafor, metaplus,\nPMCMRplus, psych, rmarkdown, spelling, survival, testthat (>=\n3.1.4), tibble, vdiffr, WRS2"
## glue "covr, crayon, DBI, dplyr, forcats, ggplot2, knitr, magrittr,\nmicrobenchmark, R.utils, rmarkdown, rprintf, RSQLite, stringr,\ntestthat (>= 3.0.0), vctrs (>= 0.3.0), waldo (>= 0.3.0), withr"
## gmp "Rmpfr, MASS, round"
## googledrive "covr, curl, downlit, dplyr (>= 1.0.0), knitr, mockr,\nrmarkdown, roxygen2, sodium, spelling, testthat (>= 3.0.0)"
## googlesheets4 "covr, readr, rmarkdown, sodium, spelling, testthat (>=\n3.1.3), withr"
## gridExtra "ggplot2, egg, lattice, knitr, testthat"
## gtable "covr, testthat, knitr, rmarkdown, ggplot2, profvis"
## haven "covr, crayon, fs, knitr, pillar (>= 1.4.0), rmarkdown,\ntestthat (>= 3.0.0)"
## hexbin "marray, affy, Biobase, limma, knitr"
## highr "knitr, markdown, testit"
## hms "crayon, lubridate, pillar (>= 1.1.0), testthat (>= 3.0.0)"
## hrbrthemes "testthat, dplyr, gridExtra, hunspell, stringi, gcookbook,\nclipr, vdiffr, svglite"
## htmltools "markdown, testthat, withr, Cairo, ragg, shiny"
## httr "covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat\n(>= 0.8.0), xml2"
## hunspell "spelling, testthat, pdftools, janeaustenr, wordcloud2, knitr,\nstopwords, rmarkdown"
## hypergeo NA
## ids "knitr, rcorpora, rmarkdown, testthat"
## insight "AER, afex, aod, BayesFactor, bayestestR, bbmle, bdsmatrix,\nbetareg, bife, biglm, blavaan, blme, boot, brms, censReg, cgam,\nclubSandwich, coxme, cplm, crch, datawizard, effectsize,\nemmeans, epiR, estimatr, feisr, fixest, fungible, gam, gamlss,\ngamm4, gbm, gee, geepack, GLMMadaptive, glmmTMB, gmnl, gt,\nhttr, ivreg, JM, knitr, lavaan, lavaSearch2, lfe, lme4,\nlmerTest, lmtest, logistf, logitr, MASS, marginaleffects,\nMatrix, mclogit, mclust, MCMCglmm, merTools, metaBMA, mgcv,\nmice, mlogit, mhurdle, multgee, nlme, nnet, nonnest2, ordinal,\npanelr, parameters, parsnip, pbkrtest, performance, plm,\npoorman, pscl, psych, quantreg, rmarkdown, rms, robustbase,\nrobustlmm, rstanarm (>= 2.21.1), rstantools, rstudioapi,\nsandwich, speedglm, splines, statmod, survey, survival,\ntestthat, truncreg, tweedie, VGAM"
## installr "curl, XML, devtools, rjson, data.table, plyr, ggplot2, sp,\ntools, pkgbuild (>= 1.1.0), testthat (>= 2.1.0), mockery,\nR.utils"
## interp "sp, Deriv, Ryacas, ggplot2, gridExtra, lattice, stringi,\nstringr"
## isoband "covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf,\ntestthat, xml2"
## jpeg NA
## jquerylib "testthat"
## jsonlite "httr, vctrs, testthat, knitr, rmarkdown, R.rsp, sf"
## knitr "markdown, formatR, testit, digest, rgl (>= 0.95.1201),\ncodetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice\n(>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1),\nmagick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>=\n0.4-1), showtext, tibble, sass, bslib, ragg, gridSVG, styler\n(>= 1.2.0), targets (>= 0.6.0)"
## kSamples NA
## labeling NA
## latticeExtra "maps, mapproj, deldir, quantreg, zoo, mgcv"
## lazyeval "knitr, rmarkdown (>= 0.2.65), testthat, covr"
## lifecycle "covr, crayon, knitr, lintr, rmarkdown, testthat (>= 3.0.1),\ntibble, tidyverse, tools, vctrs, withr"
## lubridate "covr, knitr, testthat (>= 2.1.0), vctrs (>= 0.3.0), rmarkdown"
## magrittr "covr, knitr, rlang, rmarkdown, testthat"
## mapproj NA
## maps "mapproj (>= 1.2-0), mapdata (>= 2.3.0), sp, rnaturalearth"
## maptools "rgeos (>= 0.1-8), spatstat.geom (>= 1.65-0), PBSmapping,\nmaps, RColorBrewer, raster, polyclip, plotrix, spatstat.linnet\n(>= 1.65-3), spatstat.utils (>= 1.19.0), spatstat (>= 2.0-0)"
## markdown "knitr, RCurl"
## Matrix "expm, MASS"
## MatrixModels NA
## mc2d "fitdistrplus, survival, testthat (>= 3.0.0)"
## memoise "digest, aws.s3, covr, googleAuthR, googleCloudStorageR, httr,\ntestthat"
## mime NA
## modelr "compiler, covr, ggplot2, testthat"
## multcompView "multcomp, pgirmess, MASS"
## munsell "ggplot2, testthat"
## mvtnorm NA
## openssl "curl, testthat (>= 2.1.0), digest, knitr, rmarkdown,\njsonlite, jose, sodium"
## packcircles "ggiraph, ggplot2, knitr, rmarkdown, lpSolve"
## paletteer "covr, ggplot2 (>= 3.3.0), ggthemes (>= 4.0.0), harrypotter\n(>= 2.1.0), knitr, oompaBase, palr, pals, rmarkdown, scico,\ntestthat (>= 2.1.0), vdiffr, viridisLite"
## palmerpenguins "knitr, rmarkdown, tibble, ggplot2, dplyr, tidyr, recipes"
## parameters "AER, afex, aod, BayesFactor, BayesFM, bbmle, betareg, biglm,\nblme, boot, brglm2, brms, broom, cAIC4, car, cgam,\nClassDiscovery, clubSandwich, cluster, cplm, dbscan, domir (>=\n0.2.0), drc, DRR, effectsize (>= 0.6.0), EGAnet (>= 0.7),\nemmeans (>= 1.7.0), factoextra, FactoMineR, fastICA, fixest,\nfpc, gam, gamlss, gee, geepack, ggplot2, GLMMadaptive, glmmTMB,\nGPArotation, gt, haven, httr, Hmisc, ivprobit, ivreg, knitr,\nlavaan, lavaSearch2, lfe, lm.beta, lme4, lmerTest, lmtest,\nlogspline, lqmm, M3C, magrittr, marginaleffects, MASS, Matrix,\nmclust, MCMCglmm, mediation, merDeriv, metaBMA, metafor, mfx,\nmgcv, mice, multcomp, MuMIn, NbClust, nFactors, nlme, nnet,\nopenxlsx, ordinal, panelr, pbkrtest, PCDimension, performance\n(>= 0.10.0), plm, PMCMRplus, poorman, posterior, PROreg, pscl,\npsych, pvclust, quantreg, randomForest, rmarkdown, rms,\nrstanarm, rsvd, sandwich, see (>= 0.6.9), sparsepca, survey,\nsurvival, testthat, TMB, truncreg, VGAM, WRS2"
## patchwork "knitr, rmarkdown, gridGraphics, gridExtra, ragg, testthat (>=\n2.1.0), vdiffr, covr, png"
## pbapply "shiny"
## performance "AER, afex, BayesFactor, bayesplot, betareg, bigutilsr,\nblavaan, brms, car, CompQuadForm, correlation, cplm, dbscan,\nestimatr, fixest, forecast, gamm4, ggplot2, glmmTMB, httr, ICS,\nICSOutlier, ISLR, lavaan, lme4, lmtest, loo, magrittr, MASS,\nMatrix, mclust, metafor, mgcv, mlogit, multimode, nlme,\nnonnest2, ordinal, parallel, parameters, patchwork, poorman,\npscl, psych, randomForest, rmarkdown, rstanarm, rstantools,\nsandwich, see, survey, survival, testthat, tweedie, VGAM"
## permute "vegan (>= 2.0-0), testthat (>= 0.5), parallel, knitr,\nrmarkdown, bookdown, sessioninfo"
## pillar "bit64, debugme, DiagrammeR, dplyr, formattable, ggplot2,\nknitr, lubridate, nanotime, nycflights13, palmerpenguins,\nrmarkdown, scales, stringi, survival, testthat (>= 3.1.1),\ntibble, units (>= 0.7.2), vdiffr, withr"
## pkgconfig "covr, testthat, disposables (>= 1.0.3)"
## pkgload "bitops, covr, mathjaxr, pak, pkgbuild, Rcpp, remotes,\nrstudioapi, testthat (>= 3.1.0)"
## plyr "abind, covr, doParallel, foreach, iterators, itertools,\ntcltk, testthat"
## PMCMRplus "xtable, graphics, knitr, rmarkdown, car, e1071, multcomp,\npwr, NSM3"
## png NA
## praise "testthat"
## prettyunits "codetools, covr, testthat"
## prismatic "covr, crayon, testthat (>= 3.0.0)"
## processx "callr (>= 3.7.0), cli (>= 3.3.0), codetools, covr, curl,\ndebugme, parallel, rlang (>= 1.0.2), testthat (>= 3.0.0), withr"
## progress "Rcpp, testthat, withr"
## proxy "cba"
## ps "callr, covr, curl, pillar, pingr, processx (>= 3.1.0), R6,\nrlang, testthat (>= 3.0.0),"
## purrr "covr, crayon, dplyr (>= 0.7.8), httr, knitr, rmarkdown,\ntestthat, tibble, tidyselect, vctrs"
## R6 "testthat, pryr"
## rappdirs "roxygen2, testthat (>= 3.0.0), covr, withr"
## raster "ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf,\ntinytest, gstat, fields, exactextractr"
## rasterVis "rgl, ggplot2, colorspace, dichromat, sf"
## RColorBrewer NA
## Rcpp "tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2)"
## RcppEigen "inline, tinytest, pkgKitten, microbenchmark"
## RcppParallel "Rcpp, RUnit, knitr, rmarkdown"
## readr "covr, curl, datasets, knitr, rmarkdown, spelling, stringi,\ntestthat (>= 3.1.2), tzdb (>= 0.1.1), waldo, withr, xml2"
## readxl "knitr, rmarkdown, testthat (>= 3.0.0)"
## rematch "covr, testthat"
## rematch2 "covr, testthat"
## reprex "covr, fortunes, miniUI, mockr, rprojroot, sessioninfo, shiny,\nspelling, styler (>= 1.2.0), testthat (>= 3.0.2)"
## reshape NA
## rex "covr, dplyr, ggplot2, Hmisc, knitr, magrittr, rmarkdown,\nroxygen2, rvest, stringr, testthat"
## rgdal "knitr, DBI, RSQLite, maptools, mapview, rmarkdown, curl,\nrgeos"
## rlang "cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr,\nmethods, pillar, rmarkdown, stats, testthat (>= 3.0.0), tibble,\nusethis, vctrs (>= 0.2.3), withr"
## rmarkdown "digest, dygraphs, fs, rsconnect, downlit (>= 0.4.0), katex\n(>= 1.4.0), sass (>= 0.4.0), shiny (>= 1.6.0), testthat (>=\n3.0.3), tibble, tufte, vctrs, withr (>= 2.4.2)"
## Rmpfr "MASS, Bessel, polynom, sfsmisc (>= 1.0-20), Matrix"
## rprojroot "covr, knitr, lifecycle, mockr, rmarkdown, testthat (>=\n3.0.0), withr"
## rstantools "rstan (>= 2.17.2), usethis (>= 1.5.1), testthat (>= 2.0.0),\nknitr, pkgbuild, pkgload, roxygen2 (>= 6.0.1), rmarkdown,\nrstudioapi"
## rstudioapi "testthat, knitr, rmarkdown, clipr, covr"
## Rttf2pt1 NA
## rvest "covr, knitr, readr, repurrrsive, rmarkdown, spelling, stringi\n(>= 0.3.1), testthat (>= 3.0.2), webfakes"
## s2 "testthat (>= 3.0.0), vctrs"
## sass "testthat, knitr, rmarkdown, withr, shiny, curl"
## scales "bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), stringi,\ntestthat (>= 3.0.0), waldo (>= 0.4.0)"
## selectr "testthat, XML, xml2"
## sf "blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>=\n0.2-1), maps, mapview, Matrix, microbenchmark, odbc, pbapply,\npillar, pool, raster, rlang, rmarkdown, RPostgres (>= 1.1.0),\nRPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat (>= 2.0-1),\nspatstat.geom, spatstat.random, spatstat.linnet,\nspatstat.utils, stars (>= 0.2-0), terra, testthat, tibble (>=\n1.4.1), tidyr (>= 1.2.0), tidyselect (>= 1.0.0), tmap (>= 2.0),\nvctrs, wk"
## sm "rgl, misc3d, interp, gam, tkrplot, rpanel (>= 1.1-4), tcltk"
## sp "RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat,\nmaptools, deldir, knitr, rmarkdown, sf"
## statsExpressions "afex, ggplot2, knitr, metaBMA, metafor, metaplus, PMCMRplus,\npurrr, rmarkdown, spelling, survival, testthat (>= 3.1.4),\nutils, withr"
## stringi NA
## stringr "covr, htmltools, htmlwidgets, knitr, rmarkdown, testthat"
## SuppDists "RcppZiggurat"
## svglite "htmltools, testthat, xml2 (>= 1.0.0), covr, fontquiver (>=\n0.2.0), knitr, rmarkdown"
## sys "unix (>= 1.4), spelling, testthat"
## systemfonts "testthat (>= 2.1.0), covr, knitr, rmarkdown, tools"
## terra "parallel, tinytest, ncdf4, sf (>= 0.9-8), deldir, XML,\nleaflet"
## testthat "covr, curl (>= 0.9.5), diffviewer (>= 0.1.0), knitr, mockery,\nrmarkdown, rstudioapi, shiny, usethis, vctrs (>= 0.1.0), xml2"
## tibble "bench, bit64, blob, brio, callr, cli, covr, crayon (>=\n1.3.4), DiagrammeR, dplyr, evaluate, formattable, ggplot2, hms,\nhtmltools, knitr, lubridate, mockr, nycflights13, pkgbuild,\npkgload, purrr, rmarkdown, stringi, testthat (>= 3.0.2), tidyr,\nwithr"
## tidyr "covr, data.table, jsonlite, knitr, readr, repurrrsive (>=\n1.0.0), rmarkdown, testthat (>= 3.0.0)"
## tidyselect "covr, crayon, dplyr, knitr, magrittr, rmarkdown, stringr,\ntestthat (>= 3.1.1), tibble (>= 2.1.3)"
## tidyverse "covr, feather, glue, knitr, rmarkdown, testthat"
## tinytex "testit, rstudioapi"
## tzdb "covr, testthat (>= 3.0.0)"
## units "NISTunits, measurements, xml2, magrittr, pillar (>= 1.3.0),\ndplyr (>= 1.0.0), vctrs (>= 0.3.1), ggplot2 (> 3.2.1), testthat\n(>= 3.0.0), vdiffr, knitr, rmarkdown"
## utf8 "cli, covr, knitr, rlang, rmarkdown, testthat (>= 3.0.0),\nwithr"
## uuid NA
## vctrs "bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr,\npillar (>= 1.4.4), pkgdown (>= 2.0.1), rmarkdown, testthat (>=\n3.0.0), tibble (>= 3.1.3), withr, xml2, waldo (>= 0.2.0),\nzeallot"
## vdiffr "covr, ggplot2 (>= 3.2.0), roxygen2, withr"
## vegan "parallel, tcltk, knitr, markdown"
## vioplot "base, ggplot2, RColorBrewer, knitr, rmarkdown, testthat"
## viridis "hexbin (>= 1.27.0), scales, MASS, knitr, dichromat,\ncolorspace, raster, rasterVis, httr, mapproj, vdiffr, svglite\n(>= 1.2.0), testthat, covr, rmarkdown, rgdal, maps"
## viridisLite "hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr"
## vroom "archive, bench (>= 1.1.0), covr, curl, dplyr, forcats, fs,\nggplot2, knitr, patchwork, prettyunits, purrr, rmarkdown,\nrstudioapi, scales, spelling, testthat (>= 2.1.0), tidyr,\nutils, waldo, xml2"
## waldo "covr, R6, testthat (>= 3.0.0), withr, xml2"
## withr "callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown\n(>= 2.12), RSQLite, testthat (>= 3.0.0)"
## wk "testthat (>= 3.0.0), vctrs (>= 0.3.0), sf, tibble, readr"
## WRS2 "knitr, car, ggplot2, colorspace, mediation, GGally, codetools"
## xfun "testit, parallel, codetools, rstudioapi, tinytex (>= 0.30),\nmime, markdown, knitr, htmltools, remotes, pak, rhub, renv,\ncurl, jsonlite, magick, rmarkdown"
## xml2 "covr, curl, httr, knitr, magrittr, mockery, rmarkdown,\ntestthat (>= 2.1.0)"
## yaml "RUnit"
## zeallot "testthat, knitr, rmarkdown, purrr, magrittr"
## zoo "AER, coda, chron, ggplot2 (>= 3.0.0), mondate, scales,\nstinepack, strucchange, timeDate, timeSeries, tis, tseries, xts"
## base "methods"
## boot "MASS, survival"
## class NA
## cluster "MASS, Matrix"
## codetools NA
## compiler NA
## datasets NA
## foreign NA
## graphics NA
## grDevices "KernSmooth"
## grid NA
## KernSmooth "MASS, carData"
## lattice "KernSmooth, MASS, latticeExtra"
## MASS "lattice, nlme, nnet, survival"
## Matrix "expm, MASS"
## methods "codetools"
## mgcv "parallel, survival, MASS"
## nlme "Hmisc, MASS, SASmixed"
## nnet "MASS"
## parallel "methods"
## rpart "survival"
## spatial "MASS"
## splines "Matrix, methods"
## stats "MASS, Matrix, SuppDists, methods, stats4"
## stats4 NA
## survival NA
## tcltk NA
## tools "codetools, methods, xml2, curl, commonmark, knitr, xfun,\nmathjaxr"
## translations NA
## utils "methods, xml2, commonmark, knitr"
## Enhances
## askpass NA
## assertthat NA
## backports NA
## base64enc "png"
## BayesFactor NA
## bayestestR NA
## bit NA
## bit64 NA
## blob NA
## brio NA
## broom NA
## bslib NA
## BWStest NA
## cachem NA
## callr NA
## cartogram NA
## cellranger NA
## classInt NA
## cli NA
## clipr NA
## coda NA
## colorspace NA
## contfrac NA
## correlation NA
## covr NA
## cpp11 NA
## crayon NA
## curl NA
## data.table NA
## datawizard NA
## DBI NA
## dbplyr NA
## deldir NA
## desc NA
## deSolve NA
## dichromat NA
## diffobj NA
## digest NA
## dplyr NA
## dtplyr NA
## e1071 NA
## effectsize NA
## ellipsis NA
## elliptic NA
## evaluate NA
## extrafont NA
## extrafontdb NA
## fansi NA
## farver NA
## fastmap NA
## forcats NA
## fs NA
## gargle NA
## gcookbook NA
## gdtools NA
## generics NA
## ggplot2 "sp"
## ggplot2movies NA
## ggrepel NA
## ggridges NA
## ggsignif NA
## ggstatsplot NA
## glue NA
## gmp NA
## googledrive NA
## googlesheets4 NA
## gridExtra NA
## gtable NA
## haven NA
## hexbin NA
## highr NA
## hms NA
## hrbrthemes NA
## htmltools "knitr"
## httr NA
## hunspell NA
## hypergeo NA
## ids NA
## insight NA
## installr NA
## interp "RcppEigen"
## isoband NA
## jpeg NA
## jquerylib NA
## jsonlite NA
## knitr NA
## kSamples NA
## labeling NA
## latticeExtra NA
## lazyeval NA
## lifecycle NA
## lubridate "chron, timeDate, tis, zoo"
## magrittr NA
## mapproj NA
## maps NA
## maptools "gpclib"
## markdown NA
## Matrix "MatrixModels, graph, SparseM, sfsmisc, igraph, maptools, sp,\nspdep"
## MatrixModels NA
## mc2d NA
## memoise NA
## mime NA
## modelr NA
## multcompView NA
## munsell NA
## mvtnorm NA
## openssl NA
## packcircles NA
## paletteer NA
## palmerpenguins NA
## parameters NA
## patchwork NA
## pbapply NA
## performance NA
## permute NA
## pillar NA
## pkgconfig NA
## pkgload NA
## plyr NA
## PMCMRplus NA
## png NA
## praise NA
## prettyunits NA
## prismatic NA
## processx NA
## progress NA
## proxy NA
## ps NA
## purrr NA
## R6 NA
## rappdirs NA
## raster NA
## rasterVis NA
## RColorBrewer NA
## Rcpp NA
## RcppEigen NA
## RcppParallel NA
## readr NA
## readxl NA
## rematch NA
## rematch2 NA
## reprex NA
## reshape NA
## rex NA
## rgdal NA
## rlang "winch"
## rmarkdown NA
## Rmpfr "dfoptim, pracma"
## rprojroot NA
## rstantools NA
## rstudioapi NA
## Rttf2pt1 NA
## rvest NA
## s2 NA
## sass NA
## scales NA
## selectr NA
## sf NA
## sm NA
## sp NA
## statsExpressions NA
## stringi NA
## stringr NA
## SuppDists NA
## svglite NA
## sys NA
## systemfonts NA
## terra NA
## testthat NA
## tibble NA
## tidyr NA
## tidyselect NA
## tidyverse NA
## tinytex NA
## tzdb NA
## units NA
## utf8 NA
## uuid NA
## vctrs NA
## vdiffr NA
## vegan NA
## vioplot NA
## viridis NA
## viridisLite NA
## vroom NA
## waldo NA
## withr NA
## wk NA
## WRS2 NA
## xfun NA
## xml2 NA
## yaml NA
## zeallot NA
## zoo NA
## base NA
## boot NA
## class NA
## cluster NA
## codetools NA
## compiler NA
## datasets NA
## foreign NA
## graphics NA
## grDevices NA
## grid NA
## KernSmooth NA
## lattice "chron"
## MASS NA
## Matrix "MatrixModels, graph, SparseM, sfsmisc, igraph, maptools, sp,\nspdep"
## methods NA
## mgcv NA
## nlme NA
## nnet NA
## parallel "snow, nws, Rmpi"
## rpart NA
## spatial NA
## splines NA
## stats NA
## stats4 NA
## survival NA
## tcltk NA
## tools NA
## translations NA
## utils NA
## License License_is_FOSS
## askpass "MIT + file LICENSE" NA
## assertthat "GPL-3" NA
## backports "GPL-2 | GPL-3" NA
## base64enc "GPL-2 | GPL-3" NA
## BayesFactor "GPL-2" NA
## bayestestR "GPL-3" NA
## bit "GPL-2 | GPL-3" NA
## bit64 "GPL-2 | GPL-3" NA
## blob "MIT + file LICENSE" NA
## brio "MIT + file LICENSE" NA
## broom "MIT + file LICENSE" NA
## bslib "MIT + file LICENSE" NA
## BWStest "LGPL-3" NA
## cachem "MIT + file LICENSE" NA
## callr "MIT + file LICENSE" NA
## cartogram "GPL-3" NA
## cellranger "MIT + file LICENSE" NA
## classInt "GPL (>= 2)" NA
## cli "MIT + file LICENSE" NA
## clipr "GPL-3" NA
## coda "GPL (>= 2)" NA
## colorspace "BSD_3_clause + file LICENSE" NA
## contfrac "GPL-2" NA
## correlation "GPL-3" NA
## covr "MIT + file LICENSE" NA
## cpp11 "MIT + file LICENSE" NA
## crayon "MIT + file LICENSE" NA
## curl "MIT + file LICENSE" NA
## data.table "MPL-2.0 | file LICENSE" NA
## datawizard "GPL (>= 3)" NA
## DBI "LGPL (>= 2.1)" NA
## dbplyr "MIT + file LICENSE" NA
## deldir "GPL (>= 2)" NA
## desc "MIT + file LICENSE" NA
## deSolve "GPL (>= 2)" NA
## dichromat "GPL-2" NA
## diffobj "GPL-2 | GPL-3" NA
## digest "GPL (>= 2)" NA
## dplyr "MIT + file LICENSE" NA
## dtplyr "MIT + file LICENSE" NA
## e1071 "GPL-2 | GPL-3" NA
## effectsize "GPL-3" NA
## ellipsis "MIT + file LICENSE" NA
## elliptic "GPL-2" NA
## evaluate "MIT + file LICENSE" NA
## extrafont "GPL-2" NA
## extrafontdb "GPL-2" NA
## fansi "GPL-2 | GPL-3" NA
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## utils NA NA NA "yes" "4.2.1"#install.packages("vegan", dependencies=TRUE)library(vegan)## Loading required package: permute## Loading required package: lattice## This is vegan 2.6-2#remove.packages("vegan")Project Management
- Set up management structure (i.e., “data”, “src”, “results”, “doc”)
- Discuss avoiding redundancy of files
- Make sure to use version control (i.e., Git)
Getting Help
?plot## starting httpd help server ... donehelp(plot)?"<-"vignette("FAQ-vegan")citation("vegan")##
## To cite package 'vegan' in publications use:
##
## Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P,
## O'Hara R, Solymos P, Stevens M, Szoecs E, Wagner H, Barbour M,
## Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M,
## Durand S, Evangelista H, FitzJohn R, Friendly M, Furneaux B, Hannigan
## G, Hill M, Lahti L, McGlinn D, Ouellette M, Ribeiro Cunha E, Smith T,
## Stier A, Ter Braak C, Weedon J (2022). _vegan: Community Ecology
## Package_. R package version 2.6-2,
## <https://CRAN.R-project.org/package=vegan>.
##
## A BibTeX entry for LaTeX users is
##
## @Manual{,
## title = {vegan: Community Ecology Package},
## author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
## year = {2022},
## note = {R package version 2.6-2},
## url = {https://CRAN.R-project.org/package=vegan},
## }Data and their formats
cats <- data.frame(coat = c("calico","black","tabby"),
weight = c(2.1,5,3.2),
likes_string = c(1,0,1))catsgetwd()## [1] "C:/Users/msbre/OneDrive/Documents/biol48006220_Fall2022/practcomp_2022"write.csv(cats, file = "./data/cats.csv")cats <- read.csv("./data/cats.csv")cats$coat## [1] "calico" "black" "tabby"cats$weight## [1] 2.1 5.0 3.2cats$weight*10## [1] 21 50 32log(cats$weight)## [1] 0.7419373 1.6094379 1.1631508logweight <- log(cats$weight)
cbind(cats,logweight)cats <- cbind(cats,logweight)catspaste("My cat is ", cats$coat, ", and it weighs ", cats$weight, " kg.", sep="")## [1] "My cat is calico, and it weighs 2.1 kg."
## [2] "My cat is black, and it weighs 5 kg."
## [3] "My cat is tabby, and it weighs 3.2 kg."Data Types
typeof(cats$coat)## [1] "character"typeof(cats$weight)## [1] "double"typeof(cats$likes_string)## [1] "integer"typeof(3.14159)## [1] "double"typeof(1i)## [1] "complex"typeof(FALSE)## [1] "logical"typeof(TRUE)## [1] "logical"typeof(T)## [1] "logical"typeof(F)## [1] "logical"typeof(cats)## [1] "list"class(cats)## [1] "data.frame"file.show("./data/cats.csv")cats$likes_string <- as.logical(cats$likes_string)
typeof(cats$likes_string)## [1] "logical"cats$likes_string## [1] TRUE FALSE TRUEc("a", "b")## [1] "a" "b"ab <- c("a", "b")
ab## [1] "a" "b"c(ab,"c")## [1] "a" "b" "c"c(ab, ab)## [1] "a" "b" "a" "b"1:10## [1] 1 2 3 4 5 6 7 8 9 10seq(10)## [1] 1 2 3 4 5 6 7 8 9 10z <- seq(10)
head(z, n=3)## [1] 1 2 3length(z)## [1] 10class(z)## [1] "integer"typeof(z)## [1] "integer"seq(70,100, by=5)## [1] 70 75 80 85 90 95 100Data Frames
catsstr(cats$coat)## chr [1:3] "calico" "black" "tabby"coats <- c("tabby", "tortoiseshell", "tortoiseshell", "black", "tabby")
coats## [1] "tabby" "tortoiseshell" "tortoiseshell" "black"
## [5] "tabby"str(coats)## chr [1:5] "tabby" "tortoiseshell" "tortoiseshell" "black" "tabby"factor(coats)## [1] tabby tortoiseshell tortoiseshell black tabby
## Levels: black tabby tortoiseshellcategories <- factor(coats)
class(coats)## [1] "character"class(categories)## [1] "factor"str(categories)## Factor w/ 3 levels "black","tabby",..: 2 3 3 1 2Lists
list_example <- list(title="Numbers", numbers = 1:10, data=TRUE)list_example## $title
## [1] "Numbers"
##
## $numbers
## [1] 1 2 3 4 5 6 7 8 9 10
##
## $data
## [1] TRUEanother_list <- list(1,"a",TRUE,1+1i)
another_list## [[1]]
## [1] 1
##
## [[2]]
## [1] "a"
##
## [[3]]
## [1] TRUE
##
## [[4]]
## [1] 1+1itypeof(list_example)## [1] "list"class(list_example)## [1] "list"typeof(cats)## [1] "list"class(cats)## [1] "data.frame"data.frame(list_example)catscats[,3]## [1] 2.1 5.0 3.2cats[3,]cats[2:3,c(1,3)]Matricies
matrix_example <- matrix(0, ncol=5, nrow=3)matrix_example## [,1] [,2] [,3] [,4] [,5]
## [1,] 0 0 0 0 0
## [2,] 0 0 0 0 0
## [3,] 0 0 0 0 0class(matrix_example)## [1] "matrix" "array"typeof(matrix_example)## [1] "double"str(matrix_example)## num [1:3, 1:5] 0 0 0 0 0 0 0 0 0 0 ...dim(matrix_example)## [1] 3 5ncol(matrix_example)## [1] 5nrow(matrix_example)## [1] 3class(data.frame(matrix_example))## [1] "data.frame"df_example <- data.frame(matrix_example)
df_exampleSubsetting
p <- c(2.3,6.9,4.0,23,1)
p## [1] 2.3 6.9 4.0 23.0 1.0names(p) <- c('a','b','c','d','e')
p## a b c d e
## 2.3 6.9 4.0 23.0 1.0p[1]## a
## 2.3p[2:4]## b c d
## 6.9 4.0 23.0p[c(1,5)]## a e
## 2.3 1.0p[c(1,1,1,3,5,5)]## a a a c e e
## 2.3 2.3 2.3 4.0 1.0 1.0p[6]## <NA>
## NAp[-3]## a b d e
## 2.3 6.9 23.0 1.0p[c(-1,-5)]## b c d
## 6.9 4.0 23.0p[-(2:4)]## a e
## 2.3 1.0p[c('a','c')]## a c
## 2.3 4.0p[c(T,F,T,F,T)]## a c e
## 2.3 4.0 1.0p[names(p) != 'c']## a b d e
## 2.3 6.9 23.0 1.0Factors
f <- factor(c('a','b','c','d','e'))
f## [1] a b c d e
## Levels: a b c d ef[f == 'a']## [1] a
## Levels: a b c d ef[1:3]## [1] a b c
## Levels: a b c d ef[f %in% c('b','c')]## [1] b c
## Levels: a b c d ef[-3]## [1] a b d e
## Levels: a b c d ef2 <- factor(c('a','a','b','c','c'))
f2## [1] a a b c c
## Levels: a b cf2[f2 == 'a']## [1] a a
## Levels: a b cf2[f2 %in% c('a','c')]## [1] a a c c
## Levels: a b cMatricies Resumed
set.seed(65)
m <- matrix(rnorm(6*4), ncol=4, nrow=6)
m## [,1] [,2] [,3] [,4]
## [1,] -1.1968205 -0.3943568 0.4232027 -2.34367583
## [2,] -0.9516674 -1.2484030 -1.8461725 -0.77605977
## [3,] 0.2786364 -0.6521289 -0.2456747 -2.16173144
## [4,] -1.4449411 -1.1707346 1.2538299 0.05701057
## [5,] 0.8216518 0.3604497 1.5633419 -0.24867199
## [6,] 1.2470188 1.2302708 -1.2644661 -0.07830796m[3:4, c(3,1)]## [,1] [,2]
## [1,] -0.2456747 0.2786364
## [2,] 1.2538299 -1.4449411m[,c(3,4)]## [,1] [,2]
## [1,] 0.4232027 -2.34367583
## [2,] -1.8461725 -0.77605977
## [3,] -0.2456747 -2.16173144
## [4,] 1.2538299 0.05701057
## [5,] 1.5633419 -0.24867199
## [6,] -1.2644661 -0.07830796List Revisited
xlist <- list(a="BIOL48006220",b=seq(1,10,by = 0.5), data="Grade")
xlist## $a
## [1] "BIOL48006220"
##
## $b
## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0
##
## $data
## [1] "Grade"xlist[1:2]## $a
## [1] "BIOL48006220"
##
## $b
## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0xlist['a']## $a
## [1] "BIOL48006220"xlist[['a']]## [1] "BIOL48006220"xlist['b']## $b
## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0xlist[['b']]## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0xlist$b## [1] 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0
## [16] 8.5 9.0 9.5 10.0Data Frames Revisited
gp <- read.csv('./data/forest_area_sq_km.csv')head(gp, n=10L)head(gp[3], n=10L)nrow(gp)## [1] 214head(gp[["country"]], 10L)## [1] "Aruba" "Afghanistan" "Angola"
## [4] "Albania" "Andorra" "United Arab Emirates"
## [7] "Argentina" "Armenia" "American Samoa"
## [10] "Antigua and Barbuda"gp$X2001## [1] "4.2" "12.1k" "766k" "7720" "160" "3110" "327k" "3320" "177"
## [10] "93.2" "1.31M" "38.4k" "9960" "1940" "6720" "40.4k" "71.2k" "19.1k"
## [19] "34.5k" "4" "5100" "21.1k" "83.4k" "14.5k" "10" "547k" "5.43M"
## [28] "63" "3940" "26.3k" "174k" "228k" "3.48M" "8.68" "12k" "160k"
## [37] "1.82M" "48.7k" "215k" "1.43M" "222k" "623k" "408" "403" "28.6k"
## [46] "25.3k" "129" "1720" "26.4k" "114k" "56" "479" "5750" "19.9k"
## [55] "16.5k" "136k" "605" "11.1k" "174k" "22.6k" "184k" "224k" "10.2k"
## [64] "155k" "0.8" "639" "237k" "34.6" "29.8k" "27.7k" "86.7k" "0"
## [73] "68.6k" "3460" "21.3k" "26k" "36.6k" "177" "2.2" "41.1k" "240"
## [82] "186k" "67.4k" "18.9k" "3800" "19.5k" "1.01M" "680k" "6480" "96k"
## [91] "8190" "328" "1530" "85k" "5280" "975" "249k" "31.4k" "38.9k"
## [100] "11.9k" "107k" "11.8" "110" "64.6k" "51.3" "173k" "1380" "81.6k"
## [109] "2170" "210" "67" "21.5k" "345" "20.5k" "871" "32.7k" "10"
## [118] "55.4k" "0" "3500" "129k" "8.2" "681k" "94" "9580" "133k"
## [127] "3.5" "342k" "6260" "142k" "316" "407k" "4110" "412" "30k"
## [136] "195k" "79.2k" "8380" "13k" "246k" "51.6k" "3620" "" "121k"
## [145] "58.2k" "0" "98.5k" "30" "44.3k" "44.2k" "750k" "72.2k" "398"
## [154] "363k" "91.1k" "4420" "64.1k" "32.8k" "223k" "91.2" "1490" "0"
## [163] "64k" "8.1M" "2830" "9770" "" "87.8k" "172" "25.4k" "28.9k"
## [172] "6650" "10" "73.6k" "24.8k" "" "583" "153k" "19k" "12.4k"
## [181] "281k" "4760" "" "337" "4440" "105" "61.9k" "12.6k" "192k"
## [190] "4100" "41.3k" "9460" "89.5" "2360" "6720" "203k" "10" "529k"
## [199] "30.8k" "95.2k" "14.4k" "3.05M" "30.4k" "285" "488k" "36.6" "201"
## [208] "121k" "4420" "1700" "5490" "177k" "470k" "183k"gp[c(1,3), 2:5]gp[ which(gp$X1989 <= 100 & gp$X2019 >= 100),]Conditionals and Flow
n <- 10
if (n < 10) {
print("n is less than 10")
} else if (n > 10) {
print("n is greater than 10")
} else {
print("n is equal to 10")
}## [1] "n is equal to 10"for (n in seq(0,20)) {
if (n < 10) {
print("n is less than 10")
} else if (n > 10) {
print("n is greater than 10")
} else {
print("n is equal to 10")
}
}## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is less than 10"
## [1] "n is equal to 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"
## [1] "n is greater than 10"g <- 0
while (g <=10) {
print(paste(g,"is less than or equal to 10"))
g <- g+1
}## [1] "0 is less than or equal to 10"
## [1] "1 is less than or equal to 10"
## [1] "2 is less than or equal to 10"
## [1] "3 is less than or equal to 10"
## [1] "4 is less than or equal to 10"
## [1] "5 is less than or equal to 10"
## [1] "6 is less than or equal to 10"
## [1] "7 is less than or equal to 10"
## [1] "8 is less than or equal to 10"
## [1] "9 is less than or equal to 10"
## [1] "10 is less than or equal to 10"Plotting and Figures
#install.packages("ggplot2")library(ggplot2)gp <- read.csv('data/gapminder_all.csv')
head(gp)ggplot(data=gp, mapping=aes(x=gdpPercap_1952, y=pop_1952)) + geom_point()
ggplot(data=gp, mapping=aes(x=gdpPercap_2002, y=pop_2002)) + geom_point()
gapminder <- read.csv("https://raw.githubusercontent.com/swcarpentry/r-novice-gapminder/gh-pages/_episodes_rmd/data/gapminder_data.csv")
head(gapminder)ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point()
ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country, color=continent)) + geom_line()
ggplot(data=gapminder, mapping=aes(x=year, y=lifeExp, by=country)) + geom_line(mapping=aes(color=continent)) + geom_point()
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.25) + scale_x_log10()
ggplot(data=gapminder, mapping=aes(x=gdpPercap, y=lifeExp)) + geom_point(alpha=0.25, color="purple", size = 0.9) + scale_x_log10() + geom_smooth(method = lm, color="gold", size = 1.25)## `geom_smooth()` using formula 'y ~ x'
africas <- gapminder[gapminder$continent == "Africa", ]
head(africas)ggplot(data=africas, mapping = aes(x=year, y=lifeExp)) +
geom_line(color = "red") +
facet_wrap( ~ country) +
theme(axis.text.x = element_text(angle = 90)) +
labs(
x = "Year",
y = "Life Expectency",
title = "Life Expectency Over Time in African Countries"
)
AfricanLifeExp <- ggplot(data=africas, mapping = aes(x=year, y=lifeExp)) +
geom_line(color = "red") +
facet_wrap( ~ country) +
theme(axis.text.x = element_text(angle = 90)) +
labs(
x = "Year",
y = "Life Expectency",
title = "Life Expectency Over Time in African Countries"
)ggsave(filename = "data/AfricanLifeExp.png", plot = AfricanLifeExp, width = 24, height = 40, dpi = 300, units = "cm")pdf(file = "results/AfricanLifeExp.pdf", width = 24, height = 40)
plot(AfricanLifeExp)
dev.off()## png
## 2write.table(gapminder, file="data/gapminder_web.csv", sep=",")write.csv(africas, file="data/gapminder_web_africas.csv")Fancy Plots
#install.packages(c("ggridges","viridis","hrbrthemes"), dependencies = T)library(ggridges)
library(ggplot2)
library(viridis)## Loading required package: viridisLitelibrary(hrbrthemes)## NOTE: Either Arial Narrow or Roboto Condensed fonts are required to use these themes.## Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed and## if Arial Narrow is not on your system, please see https://bit.ly/arialnarrow# Plot
ggplot(lincoln_weather, aes(x = `Mean Temperature [F]`, y = `Month`, fill = ..x..)) +
geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) +
scale_fill_viridis(name = "Temp. [F]", option = "C") +
labs(title = 'Temperatures in Lincoln NE in 2016') +
theme_ipsum() +
theme(
legend.position="none",
panel.spacing = unit(0.1, "lines"),
strip.text.x = element_text(size = 8)
)## Picking joint bandwidth of 3.37## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
## found in Windows font database
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
## found in Windows font database
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
## found in Windows font database## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font family not found in Windows font database## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
## family not found in Windows font database
#spider_data <- read.csv(file="https://wsc.nmbe.ch/resources/species_export_20221101.csv", header=TRUE)
#write.csv(spider_data, "data/spider_data_20221101.csv")
spider_data <- read.csv("data/spider_data_20221101.csv")
spider_datalibrary(ggridges)
library(ggplot2)
library(viridis)
library(hrbrthemes)
# Plot
ggplot(spider_data[1:5000,], aes(x = `year`, y = `family`)) +
geom_density_ridges(alpha=0.6, stat="binline", bins=20) +
#geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) +
labs(title = 'Spider species descriptions over time by family') +
xlab(label = "Species Description Year") +
ylab(label = "Spider Family") +
theme_ridges() +
theme(
legend.position="none",
panel.spacing = unit(0.1, "lines"),
strip.text.x = element_text(size = 8)
)
#install.packages(c("ggstatsplot","palmerpenguins","tidyverse"), dependencies=T)
library(ggstatsplot)## You can cite this package as:
## Patil, I. (2021). Visualizations with statistical details: The 'ggstatsplot' approach.
## Journal of Open Source Software, 6(61), 3167, doi:10.21105/joss.03167library(tidyverse)## ── Attaching packages
## ───────────────────────────────────────
## tidyverse 1.3.2 ──## ✔ tibble 3.1.8 ✔ dplyr 1.0.10
## ✔ tidyr 1.2.1 ✔ stringr 1.4.1
## ✔ readr 2.1.3 ✔ forcats 0.5.2
## ✔ purrr 0.3.5
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()data("penguins", package = "palmerpenguins")
penguinspenguins2 <- drop_na(penguins)
penguins2plt <- ggbetweenstats(
data = penguins,
x = species,
y = bill_length_mm
)plt
gapminder2 <- drop_na(gapminder)boxplot(gapminder2$lifeExp ~ gapminder2$continent)
#install.packages("vioplot", dependencies = T)
library(vioplot)## Loading required package: sm## Package 'sm', version 2.2-5.7: type help(sm) for summary information## Loading required package: zoo##
## Attaching package: 'zoo'## The following objects are masked from 'package:base':
##
## as.Date, as.Date.numericwith(gapminder2, vioplot(
lifeExp~continent, col = "blue"
))
plt <- ggbetweenstats(
data = gapminder2,
x = continent,
y = lifeExp
)plt
plt2 <- plt +
theme(
axis.ticks = element_blank(),
axis.line = element_line(colour = "grey50"),
panel.grid = element_line(color = "#b4aea9"),
panel.grid.minor = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.major.y = element_line(linetype = "dashed"),
panel.background = element_rect(fill = "#fbf9f4", color = "#fbf9f4"),
plot.background = element_rect(fill = "#fbf9f4", color = "#fbf9f4")
) +
labs(
x = "Continent",
y = "Life Expectency (years)",
title = "Life expectency of people living on each continent"
)plt2
ggsave(
filename = "results/gapminder_lifeExpXcontinentweb-violinplot-with-ggstatsplot.png",
plot = plt2,
width = 8,
height = 8,
device = "png"
)# Get the shape file of Africa
#install.packages("maptools")
library(maptools)## Loading required package: sp## Checking rgeos availability: FALSE
## Please note that 'maptools' will be retired by the end of 2023,
## plan transition at your earliest convenience;
## some functionality will be moved to 'sp'.
## Note: when rgeos is not available, polygon geometry computations in maptools depend on gpclib,
## which has a restricted licence. It is disabled by default;
## to enable gpclib, type gpclibPermit()data(wrld_simpl)
afr<-wrld_simpl[wrld_simpl$REGION==2,]
# We can visualize the region's boundaries with the plot function
plot(afr)
levels(penguins2$species)## [1] "Adelie" "Chinstrap" "Gentoo"penguin_matrix <- with(penguins2, cbind(bill_length_mm, bill_depth_mm, flipper_length_mm, body_mass_g))
penguin_matrix## bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
## [1,] 39.1 18.7 181 3750
## [2,] 39.5 17.4 186 3800
## [3,] 40.3 18.0 195 3250
## [4,] 36.7 19.3 193 3450
## [5,] 39.3 20.6 190 3650
## [6,] 38.9 17.8 181 3625
## [7,] 39.2 19.6 195 4675
## [8,] 41.1 17.6 182 3200
## [9,] 38.6 21.2 191 3800
## [10,] 34.6 21.1 198 4400
## [11,] 36.6 17.8 185 3700
## [12,] 38.7 19.0 195 3450
## [13,] 42.5 20.7 197 4500
## [14,] 34.4 18.4 184 3325
## [15,] 46.0 21.5 194 4200
## [16,] 37.8 18.3 174 3400
## [17,] 37.7 18.7 180 3600
## [18,] 35.9 19.2 189 3800
## [19,] 38.2 18.1 185 3950
## [20,] 38.8 17.2 180 3800
## [21,] 35.3 18.9 187 3800
## [22,] 40.6 18.6 183 3550
## [23,] 40.5 17.9 187 3200
## [24,] 37.9 18.6 172 3150
## [25,] 40.5 18.9 180 3950
## [26,] 39.5 16.7 178 3250
## [27,] 37.2 18.1 178 3900
## [28,] 39.5 17.8 188 3300
## [29,] 40.9 18.9 184 3900
## [30,] 36.4 17.0 195 3325
## [31,] 39.2 21.1 196 4150
## [32,] 38.8 20.0 190 3950
## [33,] 42.2 18.5 180 3550
## [34,] 37.6 19.3 181 3300
## [35,] 39.8 19.1 184 4650
## [36,] 36.5 18.0 182 3150
## [37,] 40.8 18.4 195 3900
## [38,] 36.0 18.5 186 3100
## [39,] 44.1 19.7 196 4400
## [40,] 37.0 16.9 185 3000
## [41,] 39.6 18.8 190 4600
## [42,] 41.1 19.0 182 3425
## [43,] 36.0 17.9 190 3450
## [44,] 42.3 21.2 191 4150
## [45,] 39.6 17.7 186 3500
## [46,] 40.1 18.9 188 4300
## [47,] 35.0 17.9 190 3450
## [48,] 42.0 19.5 200 4050
## [49,] 34.5 18.1 187 2900
## [50,] 41.4 18.6 191 3700
## [51,] 39.0 17.5 186 3550
## [52,] 40.6 18.8 193 3800
## [53,] 36.5 16.6 181 2850
## [54,] 37.6 19.1 194 3750
## [55,] 35.7 16.9 185 3150
## [56,] 41.3 21.1 195 4400
## [57,] 37.6 17.0 185 3600
## [58,] 41.1 18.2 192 4050
## [59,] 36.4 17.1 184 2850
## [60,] 41.6 18.0 192 3950
## [61,] 35.5 16.2 195 3350
## [62,] 41.1 19.1 188 4100
## [63,] 35.9 16.6 190 3050
## [64,] 41.8 19.4 198 4450
## [65,] 33.5 19.0 190 3600
## [66,] 39.7 18.4 190 3900
## [67,] 39.6 17.2 196 3550
## [68,] 45.8 18.9 197 4150
## [69,] 35.5 17.5 190 3700
## [70,] 42.8 18.5 195 4250
## [71,] 40.9 16.8 191 3700
## [72,] 37.2 19.4 184 3900
## [73,] 36.2 16.1 187 3550
## [74,] 42.1 19.1 195 4000
## [75,] 34.6 17.2 189 3200
## [76,] 42.9 17.6 196 4700
## [77,] 36.7 18.8 187 3800
## [78,] 35.1 19.4 193 4200
## [79,] 37.3 17.8 191 3350
## [80,] 41.3 20.3 194 3550
## [81,] 36.3 19.5 190 3800
## [82,] 36.9 18.6 189 3500
## [83,] 38.3 19.2 189 3950
## [84,] 38.9 18.8 190 3600
## [85,] 35.7 18.0 202 3550
## [86,] 41.1 18.1 205 4300
## [87,] 34.0 17.1 185 3400
## [88,] 39.6 18.1 186 4450
## [89,] 36.2 17.3 187 3300
## [90,] 40.8 18.9 208 4300
## [91,] 38.1 18.6 190 3700
## [92,] 40.3 18.5 196 4350
## [93,] 33.1 16.1 178 2900
## [94,] 43.2 18.5 192 4100
## [95,] 35.0 17.9 192 3725
## [96,] 41.0 20.0 203 4725
## [97,] 37.7 16.0 183 3075
## [98,] 37.8 20.0 190 4250
## [99,] 37.9 18.6 193 2925
## [100,] 39.7 18.9 184 3550
## [101,] 38.6 17.2 199 3750
## [102,] 38.2 20.0 190 3900
## [103,] 38.1 17.0 181 3175
## [104,] 43.2 19.0 197 4775
## [105,] 38.1 16.5 198 3825
## [106,] 45.6 20.3 191 4600
## [107,] 39.7 17.7 193 3200
## [108,] 42.2 19.5 197 4275
## [109,] 39.6 20.7 191 3900
## [110,] 42.7 18.3 196 4075
## [111,] 38.6 17.0 188 2900
## [112,] 37.3 20.5 199 3775
## [113,] 35.7 17.0 189 3350
## [114,] 41.1 18.6 189 3325
## [115,] 36.2 17.2 187 3150
## [116,] 37.7 19.8 198 3500
## [117,] 40.2 17.0 176 3450
## [118,] 41.4 18.5 202 3875
## [119,] 35.2 15.9 186 3050
## [120,] 40.6 19.0 199 4000
## [121,] 38.8 17.6 191 3275
## [122,] 41.5 18.3 195 4300
## [123,] 39.0 17.1 191 3050
## [124,] 44.1 18.0 210 4000
## [125,] 38.5 17.9 190 3325
## [126,] 43.1 19.2 197 3500
## [127,] 36.8 18.5 193 3500
## [128,] 37.5 18.5 199 4475
## [129,] 38.1 17.6 187 3425
## [130,] 41.1 17.5 190 3900
## [131,] 35.6 17.5 191 3175
## [132,] 40.2 20.1 200 3975
## [133,] 37.0 16.5 185 3400
## [134,] 39.7 17.9 193 4250
## [135,] 40.2 17.1 193 3400
## [136,] 40.6 17.2 187 3475
## [137,] 32.1 15.5 188 3050
## [138,] 40.7 17.0 190 3725
## [139,] 37.3 16.8 192 3000
## [140,] 39.0 18.7 185 3650
## [141,] 39.2 18.6 190 4250
## [142,] 36.6 18.4 184 3475
## [143,] 36.0 17.8 195 3450
## [144,] 37.8 18.1 193 3750
## [145,] 36.0 17.1 187 3700
## [146,] 41.5 18.5 201 4000
## [147,] 46.1 13.2 211 4500
## [148,] 50.0 16.3 230 5700
## [149,] 48.7 14.1 210 4450
## [150,] 50.0 15.2 218 5700
## [151,] 47.6 14.5 215 5400
## [152,] 46.5 13.5 210 4550
## [153,] 45.4 14.6 211 4800
## [154,] 46.7 15.3 219 5200
## [155,] 43.3 13.4 209 4400
## [156,] 46.8 15.4 215 5150
## [157,] 40.9 13.7 214 4650
## [158,] 49.0 16.1 216 5550
## [159,] 45.5 13.7 214 4650
## [160,] 48.4 14.6 213 5850
## [161,] 45.8 14.6 210 4200
## [162,] 49.3 15.7 217 5850
## [163,] 42.0 13.5 210 4150
## [164,] 49.2 15.2 221 6300
## [165,] 46.2 14.5 209 4800
## [166,] 48.7 15.1 222 5350
## [167,] 50.2 14.3 218 5700
## [168,] 45.1 14.5 215 5000
## [169,] 46.5 14.5 213 4400
## [170,] 46.3 15.8 215 5050
## [171,] 42.9 13.1 215 5000
## [172,] 46.1 15.1 215 5100
## [173,] 47.8 15.0 215 5650
## [174,] 48.2 14.3 210 4600
## [175,] 50.0 15.3 220 5550
## [176,] 47.3 15.3 222 5250
## [177,] 42.8 14.2 209 4700
## [178,] 45.1 14.5 207 5050
## [179,] 59.6 17.0 230 6050
## [180,] 49.1 14.8 220 5150
## [181,] 48.4 16.3 220 5400
## [182,] 42.6 13.7 213 4950
## [183,] 44.4 17.3 219 5250
## [184,] 44.0 13.6 208 4350
## [185,] 48.7 15.7 208 5350
## [186,] 42.7 13.7 208 3950
## [187,] 49.6 16.0 225 5700
## [188,] 45.3 13.7 210 4300
## [189,] 49.6 15.0 216 4750
## [190,] 50.5 15.9 222 5550
## [191,] 43.6 13.9 217 4900
## [192,] 45.5 13.9 210 4200
## [193,] 50.5 15.9 225 5400
## [194,] 44.9 13.3 213 5100
## [195,] 45.2 15.8 215 5300
## [196,] 46.6 14.2 210 4850
## [197,] 48.5 14.1 220 5300
## [198,] 45.1 14.4 210 4400
## [199,] 50.1 15.0 225 5000
## [200,] 46.5 14.4 217 4900
## [201,] 45.0 15.4 220 5050
## [202,] 43.8 13.9 208 4300
## [203,] 45.5 15.0 220 5000
## [204,] 43.2 14.5 208 4450
## [205,] 50.4 15.3 224 5550
## [206,] 45.3 13.8 208 4200
## [207,] 46.2 14.9 221 5300
## [208,] 45.7 13.9 214 4400
## [209,] 54.3 15.7 231 5650
## [210,] 45.8 14.2 219 4700
## [211,] 49.8 16.8 230 5700
## [212,] 49.5 16.2 229 5800
## [213,] 43.5 14.2 220 4700
## [214,] 50.7 15.0 223 5550
## [215,] 47.7 15.0 216 4750
## [216,] 46.4 15.6 221 5000
## [217,] 48.2 15.6 221 5100
## [218,] 46.5 14.8 217 5200
## [219,] 46.4 15.0 216 4700
## [220,] 48.6 16.0 230 5800
## [221,] 47.5 14.2 209 4600
## [222,] 51.1 16.3 220 6000
## [223,] 45.2 13.8 215 4750
## [224,] 45.2 16.4 223 5950
## [225,] 49.1 14.5 212 4625
## [226,] 52.5 15.6 221 5450
## [227,] 47.4 14.6 212 4725
## [228,] 50.0 15.9 224 5350
## [229,] 44.9 13.8 212 4750
## [230,] 50.8 17.3 228 5600
## [231,] 43.4 14.4 218 4600
## [232,] 51.3 14.2 218 5300
## [233,] 47.5 14.0 212 4875
## [234,] 52.1 17.0 230 5550
## [235,] 47.5 15.0 218 4950
## [236,] 52.2 17.1 228 5400
## [237,] 45.5 14.5 212 4750
## [238,] 49.5 16.1 224 5650
## [239,] 44.5 14.7 214 4850
## [240,] 50.8 15.7 226 5200
## [241,] 49.4 15.8 216 4925
## [242,] 46.9 14.6 222 4875
## [243,] 48.4 14.4 203 4625
## [244,] 51.1 16.5 225 5250
## [245,] 48.5 15.0 219 4850
## [246,] 55.9 17.0 228 5600
## [247,] 47.2 15.5 215 4975
## [248,] 49.1 15.0 228 5500
## [249,] 46.8 16.1 215 5500
## [250,] 41.7 14.7 210 4700
## [251,] 53.4 15.8 219 5500
## [252,] 43.3 14.0 208 4575
## [253,] 48.1 15.1 209 5500
## [254,] 50.5 15.2 216 5000
## [255,] 49.8 15.9 229 5950
## [256,] 43.5 15.2 213 4650
## [257,] 51.5 16.3 230 5500
## [258,] 46.2 14.1 217 4375
## [259,] 55.1 16.0 230 5850
## [260,] 48.8 16.2 222 6000
## [261,] 47.2 13.7 214 4925
## [262,] 46.8 14.3 215 4850
## [263,] 50.4 15.7 222 5750
## [264,] 45.2 14.8 212 5200
## [265,] 49.9 16.1 213 5400
## [266,] 46.5 17.9 192 3500
## [267,] 50.0 19.5 196 3900
## [268,] 51.3 19.2 193 3650
## [269,] 45.4 18.7 188 3525
## [270,] 52.7 19.8 197 3725
## [271,] 45.2 17.8 198 3950
## [272,] 46.1 18.2 178 3250
## [273,] 51.3 18.2 197 3750
## [274,] 46.0 18.9 195 4150
## [275,] 51.3 19.9 198 3700
## [276,] 46.6 17.8 193 3800
## [277,] 51.7 20.3 194 3775
## [278,] 47.0 17.3 185 3700
## [279,] 52.0 18.1 201 4050
## [280,] 45.9 17.1 190 3575
## [281,] 50.5 19.6 201 4050
## [282,] 50.3 20.0 197 3300
## [283,] 58.0 17.8 181 3700
## [284,] 46.4 18.6 190 3450
## [285,] 49.2 18.2 195 4400
## [286,] 42.4 17.3 181 3600
## [287,] 48.5 17.5 191 3400
## [288,] 43.2 16.6 187 2900
## [289,] 50.6 19.4 193 3800
## [290,] 46.7 17.9 195 3300
## [291,] 52.0 19.0 197 4150
## [292,] 50.5 18.4 200 3400
## [293,] 49.5 19.0 200 3800
## [294,] 46.4 17.8 191 3700
## [295,] 52.8 20.0 205 4550
## [296,] 40.9 16.6 187 3200
## [297,] 54.2 20.8 201 4300
## [298,] 42.5 16.7 187 3350
## [299,] 51.0 18.8 203 4100
## [300,] 49.7 18.6 195 3600
## [301,] 47.5 16.8 199 3900
## [302,] 47.6 18.3 195 3850
## [303,] 52.0 20.7 210 4800
## [304,] 46.9 16.6 192 2700
## [305,] 53.5 19.9 205 4500
## [306,] 49.0 19.5 210 3950
## [307,] 46.2 17.5 187 3650
## [308,] 50.9 19.1 196 3550
## [309,] 45.5 17.0 196 3500
## [310,] 50.9 17.9 196 3675
## [311,] 50.8 18.5 201 4450
## [312,] 50.1 17.9 190 3400
## [313,] 49.0 19.6 212 4300
## [314,] 51.5 18.7 187 3250
## [315,] 49.8 17.3 198 3675
## [316,] 48.1 16.4 199 3325
## [317,] 51.4 19.0 201 3950
## [318,] 45.7 17.3 193 3600
## [319,] 50.7 19.7 203 4050
## [320,] 42.5 17.3 187 3350
## [321,] 52.2 18.8 197 3450
## [322,] 45.2 16.6 191 3250
## [323,] 49.3 19.9 203 4050
## [324,] 50.2 18.8 202 3800
## [325,] 45.6 19.4 194 3525
## [326,] 51.9 19.5 206 3950
## [327,] 46.8 16.5 189 3650
## [328,] 45.7 17.0 195 3650
## [329,] 55.8 19.8 207 4000
## [330,] 43.5 18.1 202 3400
## [331,] 49.6 18.2 193 3775
## [332,] 50.8 19.0 210 4100
## [333,] 50.2 18.7 198 3775penguin_pca <- princomp(penguin_matrix, cor=TRUE)
summary(penguin_pca)## Importance of components:
## Comp.1 Comp.2 Comp.3 Comp.4
## Standard deviation 1.6569115 0.8821095 0.60715939 0.32845789
## Proportion of Variance 0.6863389 0.1945293 0.09216063 0.02697115
## Cumulative Proportion 0.6863389 0.8808682 0.97302885 1.00000000loadings(penguin_pca)##
## Loadings:
## Comp.1 Comp.2 Comp.3 Comp.4
## bill_length_mm 0.454 0.600 0.642 0.145
## bill_depth_mm -0.399 0.796 -0.426 -0.160
## flipper_length_mm 0.577 -0.236 -0.782
## body_mass_g 0.550 -0.592 0.585
##
## Comp.1 Comp.2 Comp.3 Comp.4
## SS loadings 1.00 1.00 1.00 1.00
## Proportion Var 0.25 0.25 0.25 0.25
## Cumulative Var 0.25 0.50 0.75 1.00biplot(penguin_pca, xlab=penguins2[,2])
penguin_pca$scores## Comp.1 Comp.2 Comp.3 Comp.4
## [1,] -1.85359302 0.032069377 -0.2349016613 0.528396625
## [2,] -1.31625406 -0.443526765 -0.0274700760 0.401726631
## [3,] -1.37660509 -0.161230478 0.1896892637 -0.528661902
## [4,] -1.88528838 -0.012351235 -0.6288726870 -0.472893203
## [5,] -1.91998074 0.817598126 -0.7010513885 -0.196416463
## [6,] -1.77302031 -0.366222957 0.0284604590 0.505368579
## [7,] -0.81849625 0.501243084 -1.3350037341 0.348259556
## [8,] -1.79895773 -0.245393945 0.6265541188 0.215177636
## [9,] -1.95614892 0.998282895 -1.0406150295 -0.210615154
## [10,] -1.56952316 0.578081948 -2.0492974540 -0.263635364
## [11,] -1.74800122 -0.610244291 -0.3648455682 0.275254393
## [12,] -1.57577371 0.086835726 -0.3623210792 -0.507079122
## [13,] -0.80472019 1.293555921 -1.0898644424 0.107519267
## [14,] -2.35017809 -0.645191072 -0.4607707684 -0.048857069
## [15,] -1.00498645 1.972422509 -0.5798770729 0.084976671
## [16,] -2.40824844 -0.308968645 0.0744441020 0.662978776
## [17,] -2.11369825 -0.136493144 -0.2723621056 0.437971409
## [18,] -1.85705729 -0.109144060 -0.8914621801 -0.007995218
## [19,] -1.50501042 -0.289127997 -0.4255462669 0.475198437
## [20,] -1.58113786 -0.603932517 0.0346978179 0.734644053
## [21,] -1.92846722 -0.297394981 -0.8633540656 0.112204664
## [22,] -1.76295054 0.138259762 0.0767052076 0.319209942
## [23,] -1.70361341 -0.187802307 0.4066389913 -0.104556344
## [24,] -2.71417458 -0.201106317 0.2389821840 0.571190457
## [25,] -1.68232816 0.285542330 -0.2438102280 0.750672188
## [26,] -1.87994963 -0.782580998 0.6638711756 0.505701001
## [27,] -1.91081367 -0.406695073 -0.3883180768 0.803391776
## [28,] -1.65683258 -0.328286332 0.2201618206 -0.106165116
## [29,] -1.51840291 0.326408242 -0.2274268406 0.501437178
## [30,] -1.44646684 -0.987685263 -0.1078452205 -0.496481192
## [31,] -1.44062410 1.059095864 -1.2903086836 -0.211391293
## [32,] -1.63466140 0.548223391 -0.8507480012 0.057249680
## [33,] -1.73335112 0.272394506 0.3372327369 0.537510640
## [34,] -2.40765908 0.067345151 -0.2101338390 0.112476774
## [35,] -1.13764744 0.357809820 -0.9521566896 1.001340496
## [36,] -2.29657080 -0.593801144 0.0354812471 0.023993523
## [37,] -0.97184877 0.117509989 -0.3164908762 -0.075207890
## [38,] -2.30890668 -0.449404139 -0.1623082340 -0.289830288
## [39,] -0.57840195 1.054586456 -0.5945824193 0.214535227
## [40,] -2.01067992 -0.997271019 0.3923067603 -0.149971631
## [41,] -0.88026262 0.212079200 -0.9751464709 0.648796919
## [42,] -1.92925587 0.342881528 0.1577848524 0.264948453
## [43,] -1.78298528 -0.657410953 -0.3574537623 -0.210018964
## [44,] -1.40940140 1.438260966 -0.8628557816 0.142277387
## [45,] -1.57392895 -0.339592411 0.1401266848 0.161823273
## [46,] -1.14654389 0.278170592 -0.6834333861 0.547546732
## [47,] -1.86608339 -0.767327681 -0.4751171379 -0.236604598
## [48,] -0.78673386 0.711147080 -0.6082512171 -0.303064057
## [49,] -2.44789222 -0.794851225 -0.1218556728 -0.498499722
## [50,] -1.26418254 0.243767425 -0.0745246189 0.002543992
## [51,] -1.54901519 -0.481769739 0.0760396714 0.198497399
## [52,] -1.22044841 0.247154032 -0.3193049336 -0.074021804
## [53,] -2.25876529 -1.189622965 0.5763198147 -0.024441402
## [54,] -1.52359256 0.034535966 -0.7173315591 -0.270413670
## [55,] -2.01615696 -1.125897262 0.1289464113 -0.075450514
## [56,] -1.13641794 1.313283236 -1.2103418754 0.082119719
## [57,] -1.57091360 -0.833767737 -0.0003422234 0.294177168
## [58,] -0.92743183 0.082527261 -0.2976685297 0.225746271
## [59,] -2.24489579 -0.996917698 0.4056666843 -0.235393033
## [60,] -0.91366065 0.046992829 -0.1219278693 0.182582152
## [61,] -1.34180687 -1.408162573 -0.0589005898 -0.437169086
## [62,] -1.24076891 0.450049108 -0.4618830617 0.412424419
## [63,] -1.80093377 -1.232829956 0.2066916214 -0.397843538
## [64,] -0.59202566 0.685886654 -0.8707826466 0.102391897
## [65,] -2.11142026 -0.472533742 -1.0002169890 -0.256856415
## [66,] -1.26934357 -0.005466398 -0.3615689854 0.174933474
## [67,] -1.02609887 -0.533157420 0.0428999873 -0.319925306
## [68,] -0.40447877 0.894152813 -0.0541870716 0.087108392
## [69,] -1.57243857 -0.850558396 -0.5136613869 -0.008978328
## [70,] -0.58666260 0.411120851 -0.3604145329 0.224356728
## [71,] -0.94042944 -0.540033074 0.2564366830 0.135633405
## [72,] -1.92733875 0.122172496 -0.7710571606 0.362408603
## [73,] -1.45634863 -1.356000198 0.0328842243 0.182033357
## [74,] -0.93751617 0.553350680 -0.3887132911 -0.024851361
## [75,] -1.96939557 -1.118922417 -0.1697294034 -0.316239385
## [76,] -0.04683282 0.100901565 -0.5018159035 0.571576618
## [77,] -1.79183530 -0.184002791 -0.6769701737 0.157556898
## [78,] -1.52578740 -0.076399251 -1.3907790578 0.021849643
## [79,] -1.68181280 -0.564107174 -0.1261078882 -0.295924034
## [80,] -1.59639832 0.908101945 -0.3946417816 -0.415078234
## [81,] -1.84348437 0.056709917 -0.9262326489 -0.077635115
## [82,] -1.85729280 -0.270705718 -0.4230718864 -0.150780390
## [83,] -1.55507132 0.168921592 -0.7194680394 0.164892744
## [84,] -1.62210133 0.040034131 -0.3215244287 -0.097029300
## [85,] -1.26523377 -0.635421240 -0.6904504308 -0.823930721
## [86,] -0.20039388 0.071188634 -0.6793241349 -0.310719775
## [87,] -2.02709537 -1.207997401 -0.2983882606 0.044893285
## [88,] -1.00562068 -0.087279300 -0.6456810644 0.820149350
## [89,] -1.87080090 -0.893881281 -0.0429811675 -0.097358865
## [90,] -0.26402770 0.363384244 -0.9384754387 -0.551385571
## [91,] -1.57962369 -0.119371375 -0.4459434375 -0.029311487
## [92,] -0.68482350 0.146252964 -0.7450419331 0.174737159
## [93,] -2.52929467 -1.762281613 0.2983518103 0.129821325
## [94,] -0.77962599 0.439581247 -0.1523402596 0.293539877
## [95,] -1.59563939 -0.740347063 -0.7112540408 -0.148374347
## [96,] -0.38617540 0.869122059 -1.3815922089 -0.047071773
## [97,] -1.80101966 -1.278444819 0.6481092793 0.108124873
## [98,] -1.51265850 0.466837670 -1.1892072983 0.248828929
## [99,] -2.00243546 -0.213819033 0.0503023889 -0.765852564
## [100,] -1.85740516 0.161221992 -0.1110276495 0.215008721
## [101,] -0.84881085 -0.622812685 -0.2725716316 -0.368699022
## [102,] -1.71870377 0.477518186 -0.8845467063 0.004937486
## [103,] -1.98479380 -0.820882689 0.4387649696 0.221911517
## [104,] -0.21353466 0.708300149 -0.8417585173 0.464363571
## [105,] -0.73824008 -0.954490503 -0.2181458163 -0.214647083
## [106,] -0.64487503 1.479361613 -0.6108640296 0.630448418
## [107,] -1.48219852 -0.354236566 0.2545966984 -0.444822833
## [108,] -0.73994061 0.753287890 -0.6997045208 0.033508069
## [109,] -1.70321099 0.915253811 -0.8882744639 -0.070646162
## [110,] -0.63280816 0.302917228 -0.2169432381 0.054822896
## [111,] -1.84273238 -0.789182569 0.5819006733 -0.355919928
## [112,] -1.60946727 0.572883733 -1.1585541611 -0.653447361
## [113,] -1.73484802 -1.064730972 -0.1073873188 -0.161648054
## [114,] -1.62792299 0.174301453 0.1999119118 -0.166383577
## [115,] -1.95305685 -0.948638014 0.0890719593 -0.198308960
## [116,] -1.66339271 0.306844796 -0.7406360661 -0.729994048
## [117,] -1.82836539 -0.565972121 0.5678134008 0.757111386
## [118,] -0.67085459 0.224468852 -0.3672406022 -0.476709049
## [119,] -1.88191000 -1.594864662 0.3433947042 -0.136018610
## [120,] -0.87699928 0.349638746 -0.6110344714 -0.280105915
## [121,] -1.56785175 -0.487347294 0.1488964877 -0.294322112
## [122,] -0.61991752 0.192001813 -0.5068659092 0.242420910
## [123,] -1.60358507 -0.689218352 0.4463019344 -0.411966916
## [124,] 0.07018089 0.333984567 -0.1682345245 -0.720380972
## [125,] -1.66069875 -0.394507052 0.0287029773 -0.234456914
## [126,] -1.13411289 0.657034153 0.0415474793 -0.481760436
## [127,] -1.68043855 -0.320534232 -0.4806643410 -0.368815057
## [128,] -0.70838734 -0.148385164 -1.2171086476 0.023568081
## [129,] -1.68833943 -0.551677888 0.0236154471 0.019658835
## [130,] -0.97035514 -0.216004046 -0.0019437648 0.285344477
## [131,] -1.88183815 -0.889082390 -0.1323725075 -0.443985421
## [132,] -1.10935310 0.749111595 -0.8947773093 -0.454253495
## [133,] -1.65603365 -1.121194594 0.1845328627 0.173444263
## [134,] -0.80493412 -0.173395579 -0.5614993590 0.302489564
## [135,] -1.18214807 -0.523204908 0.2961621018 -0.237292684
## [136,] -1.36523239 -0.434095818 0.3675952302 0.155013118
## [137,] -1.97590114 -2.096744245 0.0315182628 -0.297658915
## [138,] -1.02176382 -0.479069974 0.1880643363 0.188109106
## [139,] -1.67693429 -1.001892051 0.3311686937 -0.525003382
## [140,] -1.76540033 0.013221756 -0.2405506415 0.229507985
## [141,] -1.11219725 0.053843874 -0.7213062471 0.399901662
## [142,] -2.06481174 -0.389108766 -0.3123093029 0.118713766
## [143,] -1.55660384 -0.695834197 -0.4201502001 -0.481272180
## [144,] -1.34524467 -0.348806583 -0.4603769023 -0.127895970
## [145,] -1.57336339 -0.958805742 -0.3175980725 0.204475211
## [146,] -0.61830340 0.246934847 -0.4306022445 -0.327271339
## [147,] 1.59356859 -1.341795728 0.7216766759 0.030873935
## [148,] 2.89205390 0.464090012 -0.6944660890 -0.306550426
## [149,] 1.55157173 -0.696759932 0.8863745985 0.046321767
## [150,] 2.62068561 0.013723319 -0.2538154127 0.453430729
## [151,] 2.23455895 -0.563287236 -0.1132144676 0.396018085
## [152,] 1.55889027 -1.172013776 0.6838475283 0.109349077
## [153,] 1.45637702 -0.823329213 0.1153440662 0.116576029
## [154,] 2.02554963 -0.355648737 -0.3126368365 -0.061919459
## [155,] 1.16950299 -1.578917638 0.4562481741 -0.020797935
## [156,] 1.81451188 -0.310575391 -0.2182450616 0.119754394
## [157,] 1.28618821 -1.695400271 -0.1594576306 -0.206581987
## [158,] 2.16995116 0.253134960 -0.4222366808 0.356325763
## [159,] 1.66843953 -1.189783321 0.3817938970 -0.084288071
## [160,] 2.50595964 -0.392893307 -0.3381921739 0.848155795
## [161,] 1.03819687 -0.836838135 0.6208715802 -0.253242371
## [162,] 2.52237724 0.153089665 -0.5379832461 0.559118608
## [163,] 0.91148075 -1.704680397 0.4487569003 -0.301172786
## [164,] 3.08806126 -0.015907257 -0.8401489185 0.700860650
## [165,] 1.46071532 -0.776714255 0.2648705743 0.257731106
## [166,] 2.45853762 -0.201291445 -0.1950086762 -0.051032395
## [167,] 2.81995631 -0.328714403 -0.0353862428 0.531938971
## [168,] 1.75334566 -0.876120401 -0.1129783445 0.038667490
## [169,] 1.37704625 -0.780126191 0.5270828658 -0.248688163
## [170,] 1.62341756 -0.213079172 -0.2900987733 0.001210565
## [171,] 1.85465371 -1.684814420 -0.0686654454 0.094031942
## [172,] 1.78304339 -0.513745958 -0.1988446060 0.089180675
## [173,] 2.32062326 -0.315071902 -0.3819542242 0.542477550
## [174,] 1.57198405 -0.656470332 0.6738346178 0.125846699
## [175,] 2.58027529 0.040776239 -0.1988132596 0.224461717
## [176,] 2.23324413 -0.283702741 -0.3294490937 -0.177238602
## [177,] 1.17069843 -1.281415156 0.0033792361 0.119015362
## [178,] 1.45779016 -0.874674010 -0.0148150986 0.522045203
## [179,] 3.78701834 1.836015387 0.0259209120 0.146270932
## [180,] 2.33349180 -0.298646309 0.0979600949 -0.049690133
## [181,] 2.14182216 0.255556267 -0.4932283607 -0.008481200
## [182,] 1.59133864 -1.480424422 -0.1633554929 0.112655586
## [183,] 1.46271619 0.206122550 -1.0531652424 -0.249352525
## [184,] 1.11168166 -1.426162233 0.5489718459 0.001063615
## [185,] 1.75972697 0.035865574 -0.0887551819 0.682453101
## [186,] 0.70989154 -1.566604094 0.6687488536 -0.332516565
## [187,] 2.71361148 0.296581645 -0.5922143371 -0.013402080
## [188,] 1.24766590 -1.246707231 0.6833377467 -0.120622445
## [189,] 1.89611421 -0.202401218 0.4753572955 -0.120040069
## [190,] 2.58249171 0.339509176 -0.3036532099 0.077206232
## [191,] 1.76453362 -1.292626014 -0.1196844123 -0.136892736
## [192,] 1.15532939 -1.153251761 0.7371587302 -0.204291638
## [193,] 2.60359333 0.326484463 -0.2438662115 -0.199507546
## [194,] 1.96619306 -1.375315362 0.0834929746 0.315414369
## [195,] 1.70292714 -0.310211734 -0.6035250877 0.153770437
## [196,] 1.63023914 -0.849052487 0.3232317817 0.273246100
## [197,] 2.52824538 -0.633769450 0.0685502714 0.100367351
## [198,] 1.15735133 -0.975741632 0.4346202685 -0.110144367
## [199,] 2.47953715 -0.119944640 0.1983594951 -0.427837195
## [200,] 1.90404533 -0.771411353 0.1132635463 -0.100456128
## [201,] 1.80265515 -0.515867852 -0.4407921010 -0.280206936
## [202,] 0.99999485 -1.331427058 0.4972729927 -0.065011363
## [203,] 1.89119896 -0.627629575 -0.2585404286 -0.270745548
## [204,] 0.93091910 -1.140164212 0.1863460101 -0.020674379
## [205,] 2.77838403 0.086397319 -0.2192291925 0.011587521
## [206,] 1.07656958 -1.216553531 0.7690218627 -0.089722194
## [207,] 2.21598059 -0.562234490 -0.3921871419 -0.081715488
## [208,] 1.47355252 -1.110593355 0.5460128412 -0.277039706
## [209,] 3.37817705 0.689442994 -0.0386535780 -0.235676050
## [210,] 1.83216652 -0.947529000 0.1876661551 -0.359998860
## [211,] 2.77396146 0.644562815 -0.8262745946 -0.352529284
## [212,] 2.89794904 0.377737157 -0.7883709304 -0.183112157
## [213,] 1.68225824 -1.199923878 -0.0998299295 -0.477022930
## [214,] 2.82297979 -0.002514949 -0.1020943607 0.099837362
## [215,] 1.73822780 -0.411243001 0.2517968820 -0.170552774
## [216,] 1.88543725 -0.285343544 -0.2994447079 -0.351489667
## [217,] 2.10338085 -0.077983097 -0.1612492724 -0.230913899
## [218,] 2.02796808 -0.580915426 -0.1941530395 0.085179370
## [219,] 1.59601675 -0.558889916 0.1356338140 -0.241474911
## [220,] 2.90496724 0.198243239 -0.8678279570 -0.246651648
## [221,] 1.49289256 -0.774316869 0.6299957418 0.171246214
## [222,] 2.77638908 0.609393449 -0.6171290897 0.499629777
## [223,] 1.73279991 -1.172343176 0.2343707570 -0.083551592
## [224,] 2.35528428 -0.002138394 -1.3468098137 0.130650040
## [225,] 1.70570972 -0.473358039 0.6842810220 0.039935259
## [226,] 2.69998725 0.427945010 0.0871080008 0.137930023
## [227,] 1.61251537 -0.610214911 0.3889994769 0.059328963
## [228,] 2.48664340 0.266357334 -0.2490282583 -0.193284064
## [229,] 1.58421835 -1.206558986 0.2496827066 0.076104055
## [230,] 2.60478500 0.946598161 -0.7095477675 -0.327572783
## [231,] 1.48255754 -1.140270621 -0.0475673172 -0.456913588
## [232,] 2.65819078 -0.286338576 0.4100931985 0.278429004
## [233,] 1.84514307 -0.827905113 0.4202988503 0.219864045
## [234,] 2.82194749 0.964088245 -0.4885612022 -0.416729460
## [235,] 1.94077693 -0.413378481 0.0473262843 -0.142180870
## [236,] 2.62497748 1.000478450 -0.3543114285 -0.419531459
## [237,] 1.49201527 -0.857170341 0.1686945693 0.035129012
## [238,] 2.60960622 0.320912437 -0.5719661997 -0.004676691
## [239,] 1.51912978 -0.875767080 -0.0996184205 -0.046753911
## [240,] 2.57359526 0.259869947 -0.0349299064 -0.376587531
## [241,] 1.83678033 0.116188362 0.1497856708 -0.063153117
## [242,] 2.08569057 -0.646771800 0.0510666206 -0.403652536
## [243,] 1.29687923 -0.594513353 0.7754047121 0.532351673
## [244,] 2.42913431 0.621116375 -0.1928012220 -0.341432684
## [245,] 1.99672542 -0.312558491 0.2217179796 -0.244193976
## [246,] 3.08946906 1.385699786 -0.0444990538 -0.167589013
## [247,] 1.70781430 -0.242760558 -0.0640372566 -0.005006547
## [248,] 2.86192618 -0.181068897 -0.3379080453 -0.258446028
## [249,] 1.91173444 0.006149393 -0.6274264661 0.317353668
## [250,] 1.01903506 -1.199453811 -0.2511966283 -0.006767678
## [251,] 2.68593517 0.611780499 0.1466360279 0.293707440
## [252,] 1.12616049 -1.319740768 0.2143898775 0.113547949
## [253,] 1.97540337 -0.258352741 -0.1566904922 0.768501127
## [254,] 2.10123089 0.001282137 0.3539474001 0.069426378
## [255,] 3.08631267 0.303503990 -0.7985043802 -0.041656987
## [256,] 1.15660747 -0.802661928 -0.1614900248 -0.203567418
## [257,] 2.87996707 0.609944432 -0.3707737447 -0.412115231
## [258,] 1.58107282 -0.975789324 0.5293228946 -0.465823325
## [259,] 3.47928847 0.917457141 -0.1398153361 -0.037484214
## [260,] 2.68799274 0.316920939 -0.8998403289 0.334860941
## [261,] 1.99771558 -0.976771459 0.3794253741 0.160891982
## [262,] 1.83265107 -0.784509926 0.2407576869 -0.008954681
## [263,] 2.75150503 0.266555715 -0.4193064963 0.236255616
## [264,] 1.71385366 -0.725875158 -0.2627638239 0.330003607
## [265,] 2.01853683 0.336553720 -0.1553307198 0.438801730
## [266,] -0.79383685 0.502297056 0.8074717194 -0.006263220
## [267,] -0.38936897 1.574561014 0.5109350312 0.024047021
## [268,] -0.51502737 1.570962440 0.9634704813 0.068832652
## [269,] -1.19537904 0.706041689 0.5538823005 0.141122670
## [270,] -0.30431264 1.976580378 0.8755879471 -0.111708766
## [271,] -0.32661407 0.364192175 0.2437486903 -0.040707548
## [272,] -1.63592055 0.550237855 1.1156219629 0.559180992
## [273,] -0.07884522 1.177214867 1.0389422187 -0.000630709
## [274,] -0.47029390 0.915308965 0.0030862451 0.204179744
## [275,] -0.41681894 1.861224202 0.6907333946 -0.231118519
## [276,] -0.51891409 0.501742105 0.6032269807 0.166815460
## [277,] -0.57835220 2.072634175 0.6634603831 0.025036020
## [278,] -0.78230803 0.330433534 0.9671293681 0.592406715
## [279,] 0.36958854 1.243850743 0.8546845431 0.020768014
## [280,] -0.71249870 0.118722739 0.8886566840 0.209139614
## [281,] -0.05947710 1.686344097 0.3533619883 -0.141095628
## [282,] -0.83489700 1.753343762 0.8626797357 -0.500845897
## [283,] -0.13457112 1.740319305 2.2206319520 1.067695406
## [284,] -1.06082686 0.769161630 0.7146591809 0.009545205
## [285,] 0.10859952 1.007379727 0.3471986083 0.527984264
## [286,] -1.39779585 -0.186348140 0.5669577641 0.620899621
## [287,] -0.65604675 0.550241661 1.2198880962 0.062592917
## [288,] -1.42052018 -0.445944135 1.2266431861 -0.145219516
## [289,] -0.51123467 1.589268694 0.7273978255 0.143040457
## [290,] -0.79029911 0.506500522 0.9275907132 -0.314020685
## [291,] 0.09043496 1.616127759 0.6536706908 0.243806976
## [292,] -0.30154522 1.138218559 1.1084854655 -0.460320942
## [293,] -0.23294271 1.309290553 0.5664965313 -0.244814142
## [294,] -0.68633547 0.469421229 0.6870335877 0.200530930
## [295,] 0.55717482 2.150323559 0.1018926022 0.027621633
## [296,] -1.40654483 -0.670221602 0.7352215008 0.011798409
## [297,] 0.17536866 2.602706589 0.3448578835 0.041487132
## [298,] -1.19133191 -0.439598103 0.7914297748 0.155285519
## [299,] 0.26104673 1.422954986 0.5148950431 -0.138137453
## [300,] -0.47796571 1.148220323 0.9081987557 -0.073025324
## [301,] 0.07449111 0.207746781 0.7508551146 0.009524945
## [302,] -0.42067055 0.819697344 0.5420745640 0.077345952
## [303,] 0.72563877 2.371672611 -0.4121724661 -0.148154789
## [304,] -1.04370429 -0.056204926 1.7248433528 -0.471681487
## [305,] 0.60145456 2.182018872 0.2427114514 0.018003109
## [306,] 0.13875967 1.475189813 0.1202878446 -0.748457372
## [307,] -0.84112440 0.319554637 0.8327470142 0.406758477
## [308,] -0.47268692 1.478234974 0.9610479754 -0.174022220
## [309,] -0.52941438 0.029613649 0.8172235556 -0.183166188
## [310,] -0.14369340 1.004228137 1.1289116679 0.014467968
## [311,] 0.46216056 1.311956932 0.3324732660 0.247222379
## [312,] -0.64548540 0.887659748 1.3383991535 0.128477659
## [313,] 0.44018437 1.549794413 -0.1927032048 -0.613818246
## [314,] -0.91770719 1.349966710 1.4908954736 0.159187673
## [315,] -0.03089919 0.641199552 1.0956723098 -0.077736378
## [316,] -0.18758203 0.057047468 1.3312659872 -0.360143649
## [317,] 0.06871159 1.532811438 0.6627886634 -0.141096109
## [318,] -0.62896358 0.181340228 0.7528030542 0.038106865
## [319,] 0.01928271 1.749645867 0.3214988558 -0.255665072
## [320,] -1.31309930 -0.196650725 0.6614987783 0.106491442
## [321,] -0.33092531 1.490556293 1.2357041816 -0.243662598
## [322,] -0.85016994 -0.191170114 1.1368934124 -0.061031001
## [323,] -0.13764377 1.676744907 0.1134597978 -0.309149652
## [324,] -0.05175015 1.306076998 0.6584305849 -0.321693731
## [325,] -1.07351711 1.013945225 0.3246068883 -0.245749300
## [326,] 0.21487470 1.792293937 0.5289929168 -0.447850584
## [327,] -0.50588514 -0.018580429 1.0861560589 0.392279094
## [328,] -0.45146163 0.065448902 0.7472285907 -0.012889508
## [329,] 0.55347452 2.347611631 0.8692449423 -0.388079949
## [330,] -0.73991356 0.248154967 0.3160666932 -0.733777565
## [331,] -0.36788976 0.991079624 0.8879961032 0.195862570
## [332,] 0.49235960 1.484849279 0.3299597904 -0.550859059
## [333,] -0.21341684 1.261553796 0.7659666942 -0.108233342Statistics
Additional ways of importing/reading and manipulating data
rand <- c(12, 54, 98, 65, 38)
rand## [1] 12 54 98 65 38sum(rand)## [1] 267length(rand)## [1] 5avg.rand <- sum(rand)/length(rand)
avg.rand## [1] 53.4mean(rand)## [1] 53.4sort(rand)## [1] 12 38 54 65 98min(rand)## [1] 12max(rand)## [1] 98cumsum(rand)## [1] 12 66 164 229 267diff(rand)## [1] 42 44 -33 -27rand[2]## [1] 54rand*2## [1] 24 108 196 130 76pedes <- scan()pedes## numeric(0)Analyses
Univariate Statistics
- Categorical Data
- Barplots
beer <- c(3, 4, 1, 1, 3, 4, 3, 3, 1, 3, 2, 1, 2, 1, 2, 3, 2, 3, 1, 1, 1, 1, 4, 3, 1)
length(beer)## [1] 25barplot(beer) # WRONG
table(beer)## beer
## 1 2 3 4
## 10 4 8 3barplot(table(beer), xlab="Beer", ylab="Frequency") # Counts
barplot(table(beer)/length(beer), xlab="Beer", ylab="Proportion") # Proportions instead of frequencies
- Pie Charts
pie(table(beer), main="Beer preference by students")
- Numerical Data
- Stem-and-leaf Plots
#stem(pedes)- Strip Chart
#stripchart(pedes, method="stack")- Measures of Center
- Mean
mean(pedes)## [1] NaNmean(gapminder2$lifeExp)## [1] 59.47444- Median
median(pedes)## [1] NAmedian(gapminder$lifeExp)## [1] 60.7125with(gapminder, median(lifeExp))## [1] 60.7125- Mode
which(table(pedes) == max(table(pedes)))## Warning in max(table(pedes)): no non-missing arguments to max; returning -Inf## integer(0)- Variation
- Range
range(pedes)## Warning in min(x): no non-missing arguments to min; returning Inf## Warning in max(x): no non-missing arguments to max; returning -Inf## [1] Inf -Infdiff(range(pedes))## Warning in min(x): no non-missing arguments to min; returning Inf## Warning in max(x): no non-missing arguments to max; returning -Inf## [1] -Inf- Variance
var(pedes)## [1] NAsd(pedes)## [1] NA- IQRs
IQR(pedes)## [1] NA- Z-scores
scale(pedes)## [,1]
## attr(,"scaled:center")
## [1] NaN
## attr(,"scaled:scale")
## [1] 0- Summary
summary(pedes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## - Plots
- Histograms
#hist(pedes, breaks="scott")#hist(pedes, breaks = "scott", prob=TRUE)#hist(pedes, breaks = 5, prob=TRUE)
#lines(density(pedes))#plot(density(pedes))- Box Plots
#boxplot(pedes)summary(pedes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## Bivariate and Multivariate Statistics
- Plotting and Regression
- Box Plotting
spid.gen <- read.csv("data/spider_genitalia.csv", header = T)
spid.genboxplot(spid.gen$left.bulb/spid.gen$carapace.length ~ spid.gen$habitat)